US20170166608A1

US20170166608A1 - Precipitable peptides

Info

Publication number: US20170166608A1
Application number: US15/377,243
Authority: US
Inventors: Scott Banta; Oren SHUR
Original assignee: Columbia University in the City of New York
Current assignee: Columbia University in the City of New York
Priority date: 2011-04-13
Filing date: 2016-12-13
Publication date: 2017-06-15
Anticipated expiration: 2032-04-12
Also published as: US10358461B2; WO2012154368A1; US9550805B2; US20140187746A1

Abstract

The invention is directed to a Ca2+ precipitable polypeptide tags and cassettes useful for purification of molecules from heterogeneous samples. The invention also relates to methods for bioseparation of molecules comprising Ca2+ precipitable tags and cassettes.

Description

CROSS-REFERENCE TO RELATED APPLICATION(S)

This application is a continuation of U.S. patent application Ser. No. 14/052,367, filed Oct. 11, 2013, which is a continuation-in-part of International Application No. PCT/US2012/033293, filed Apr. 12, 2012, which claims priority to U.S. provisional application Ser. No. 61/475,042 filed Apr. 13, 2011, and also claims the benefit of and priority to U.S. provisional application Ser. No. 61/616,341 filed Mar. 27, 2012, the disclosures of all of which are hereby incorporated by reference in their entireties for all purposes.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under grant number W9132T-08-2-0012 awarded by the DTRA and under grant number W9132T-08-2-0002 awarded by the US Army. The government has certain rights in the invention.
This patent disclosure contains material that is subject to copyright protection. The copyright owner has no objection to the facsimile reproduction by anyone of the patent document or the patent disclosure as it appears in the U.S. Patent and Trademark Office patent file or records, but otherwise reserves any and all copyright rights.
All patents, patent applications and publications cited herein are hereby incorporated by reference in their entirety. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art as known to those skilled therein as of the date of the invention described herein.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Nov. 23, 2016, is named Seq.txt and is 328 KB in size.

BACKGROUND OF THE INVENTION

Rapid protein purification is an important requirement in many bioengineering applications where significant amounts of time are currently spent purifying proteins from heterogeneous samples. There are currently a number of approaches for performing bioseparation, but these approaches are expensive, time consuming, can require specialized treatments.
A variety of approaches currently exist for purifying recombinant proteins such as using a poly-histidine tag, glutathione S-transferase (GST) fusions or fusion to an elastin-like peptide (ELP). In the case of ELPs, a fusion protein can be precipitated from solution by increasing the temperature of the sample (Banki, et al., Nat Meth, vol. 2, no. 9, pp. 659-662, 2005; Fong et al, Trends in Biotechnology, vol. 28, no. 5, pp. 272-279, May. 2010). One limitation of ELP technology is that increased temperature can adversely affect the stability of fusion proteins. Another limitation of ELP technology is that inducing temperature changes are difficult in large scale preparations.
There is a need for improved purification methods for rapid purification of molecules (e.g. exogenously expressed proteins) from heterogeneous samples in a rapid manner and with high levels of recovery. This invention addresses these needs.

SUMMARY

In certain aspects, the invention relates to a precipitable beta roll cassette (PBRC) comprising one or more beta roll tags (PBRTs) wherein the one or more PBRTs comprise the amino acid sequence of SEQ ID NO: 1.
In certain aspects, the invention relates to a precipitable beta roll cassette (PBRC) comprising one or more beta roll tags (PBRTs) wherein the one or more PBRTs are independently any of: (a) a polypeptide having the amino acid sequence of SEQ ID NO: 1, or (b) a polypeptide having the amino acid sequence of any of SEQ ID NOs: 25-1337.
In certain aspects, the invention relates to a precipitable beta roll cassette (PBRC) comprising one or more beta roll tags (PBRTs) wherein the one or more PBRTs are independently any of: (a) a polypeptide having the amino acid sequence of SEQ ID NO: 1, or (b) a polypeptide having the amino acid sequence of any of SEQ ID NOs 25-1337, (c) a polypeptide comprising the amino acid sequence GXXXXXXXX (SEQ ID NO: 1343), wherein, (i) the X at position 2 is an amino acid selected from the group consisting of glycine, asparagine or aspartic acid, and (ii) the X at position 3 is an amino acid selected from the group consisting of alanine, serine, glycine, aspartic acid, glutamic acid, leucine or asparagine, and (iii) the X at position 4 is an amino acid selected from the group consisting of glycine or alanine, and (iv) the X at position 5 is an amino acid selected from the group consisting of asparagine, aspartic acid, alanine, or serine, and (v) the X at position 6 is an amino acid selected from the group consisting of aspartic acid or asparagine, (vi) the X at position 7 is an amino acid selected from the group consisting of threonine, isoleucine, valine, or leucine, and (vii) the X at position 8 is an amino acid selected from the group consisting of leucine, isoleucine, or phenylalanine, and (viii) the X at position 9 is an amino acid selected from the group consisting of tyrosine, isoleucine, valine, phenylalanine, threonine, asparagine, aspartic acid, lysine or serine.
In certain aspects, the invention relates to a precipitable beta roll cassette (PBRC) comprising one or more beta roll tags (PBRTs) wherein the one or more PBRTs are independently any of: (a) a polypeptide having the amino acid sequence of SEQ ID NO: 1, or (b) a polypeptide having the amino acid sequence of any of SEQ ID NOs 25-1337, (c) a polypeptide comprising the amino acid sequence GXXXXXXXX (SEQ ID NO: 1343), wherein, (i) the X at position 2 is an amino acid selected from the group consisting of glycine, asparagine or aspartic acid, and (ii) the X at position 3 is an amino acid selected from the group consisting of alanine, serine, glycine, aspartic acid, glutamic acid, leucine or asparagine, and (iii) the X at position 4 is an amino acid selected from the group consisting of glycine or alanine, and (iv) the X at position 5 is an amino acid selected from the group consisting of asparagine, aspartic acid, alanine, or serine, and (v) the X at position 6 is an amino acid selected from the group consisting of aspartic acid or asparagine, (vi) the X at position 7 is an amino acid selected from the group consisting of threonine, isoleucine, valine, or leucine, and (vii) the X at position 8 is an amino acid selected from the group consisting of leucine, isoleucine, or phenylalanine, and (viii) the X at position 9 is an amino acid selected from the group consisting of tyrosine, isoleucine, valine, phenylalanine, threonine, asparagine, aspartic acid, lysine or serine, or (c) a variant PBRT.
In certain aspects, the invention relates to a precipitable beta roll cassette (PBRC) comprising one or more beta roll tags (PBRTs) wherein the one or more PBRTs are independently any of: (a) a polypeptide having the amino acid sequence of SEQ ID NO: 1, or (b) a polypeptide having the amino acid sequence of any of SEQ ID NOs 25-1337, (c) a polypeptide comprising the amino acid sequence GXXXXXXXX (SEQ ID NO: 1343), wherein, (i) the X at position 2 is an amino acid selected from the group consisting of glycine, asparagine or aspartic acid, and (ii) the X at position 3 is an amino acid selected from the group consisting of alanine, serine, glycine, aspartic acid, glutamic acid, leucine or asparagine, and (iii) the X at position 4 is an amino acid selected from the group consisting of glycine or alanine, and (iv) the X at position 5 is an amino acid selected from the group consisting of asparagine, aspartic acid, alanine, or serine, and (v) the X at position 6 is an amino acid selected from the group consisting of aspartic acid or asparagine, (vi) the X at position 7 is an amino acid selected from the group consisting of threonine, isoleucine, valine, or leucine, and (vii) the X at position 8 is an amino acid selected from the group consisting of leucine, isoleucine, or phenylalanine, and (viii) the X at position 9 is an amino acid selected from the group consisting of tyrosine, isoleucine, valine, phenylalanine, threonine, asparagine, aspartic acid, lysine or serine, or (c) a variant PBRT, wherein the PBRC further comprises a capping sequence.
In certain aspects, the invention relates to a precipitable beta roll cassette (PBRC) comprising one or more beta roll tags (PBRTs) wherein the one or more PBRTs are independently any of: (a) a polypeptide having the amino acid sequence of SEQ ID NO: 1, or (b) a polypeptide having the amino acid sequence of any of SEQ ID NOs 25-1337, (c) a polypeptide comprising the amino acid sequence GXXXXXXXX (SEQ ID NO: 1343), wherein, (i) the X at position 2 is an amino acid selected from the group consisting of glycine, asparagine or aspartic acid, and (ii) the X at position 3 is an amino acid selected from the group consisting of alanine, serine, glycine, aspartic acid, glutamic acid, leucine or asparagine, and (iii) the X at position 4 is an amino acid selected from the group consisting of glycine or alanine, and (iv) the X at position 5 is an amino acid selected from the group consisting of asparagine, aspartic acid, alanine, or serine, and (v) the X at position 6 is an amino acid selected from the group consisting of aspartic acid or asparagine, (vi) the X at position 7 is an amino acid selected from the group consisting of threonine, isoleucine, valine, or leucine, and (vii) the X at position 8 is an amino acid selected from the group consisting of leucine, isoleucine, or phenylalanine, and (viii) the X at position 9 is an amino acid selected from the group consisting of tyrosine, isoleucine, valine, phenylalanine, threonine, asparagine, aspartic acid, lysine or serine, or (c) a variant PBRT, wherein the PBRC further comprises a stabilizing polypeptide.
In certain aspects, the invention relates to a PBRC linked purification moiety comprising a precipitable beta roll cassette (PBRC) comprising one or more beta roll tags (PBRTs) wherein the one or more PBRTs are independently any of: (a) a polypeptide having the amino acid sequence of SEQ ID NO: 1, or (b) a polypeptide having the amino acid sequence of any of SEQ ID NOs 25-1337, (c) a polypeptide comprising the amino acid sequence GXXXXXXXX (SEQ ID NO: 1343), wherein, (i) the X at position 2 is an amino acid selected from the group consisting of glycine, asparagine or aspartic acid, and (ii) the X at position 3 is an amino acid selected from the group consisting of alanine, serine, glycine, aspartic acid, glutamic acid, leucine or asparagine, and (iii) the X at position 4 is an amino acid selected from the group consisting of glycine or alanine, and (iv) the X at position 5 is an amino acid selected from the group consisting of asparagine, aspartic acid, alanine, or serine, and (v) the X at position 6 is an amino acid selected from the group consisting of aspartic acid or asparagine, (vi) the X at position 7 is an amino acid selected from the group consisting of threonine, isoleucine, valine, or leucine, and (vii) the X at position 8 is an amino acid selected from the group consisting of leucine, isoleucine, or phenylalanine, and (viii) the X at position 9 is an amino acid selected from the group consisting of tyrosine, isoleucine, valine, phenylalanine, threonine, asparagine, aspartic acid, lysine or serine, or (c) a variant PBRT. In certain embodiments, the PBRC is linked to the purification moiety by a peptide bond. In certain embodiments, the PBRC is linked to the purification moiety by a chemical bond that is not a peptide bond.
In certain aspects, the invention relates to a PBRC linked purification moiety comprising a precipitable beta roll cassette (PBRC) comprising one or more beta roll tags (PBRTs) wherein the one or more PBRTs are independently any of: (a) a polypeptide having the amino acid sequence of SEQ ID NO: 1, or (b) a polypeptide having the amino acid sequence of any of SEQ ID NOs 25-1337, (c) a polypeptide comprising the amino acid sequence GXXXXXXXX (SEQ ID NO: 1343), wherein, (i) the X at position 2 is an amino acid selected from the group consisting of glycine, asparagine or aspartic acid, and (ii) the X at position 3 is an amino acid selected from the group consisting of alanine, serine, glycine, aspartic acid, glutamic acid, leucine or asparagine, and (iii) the X at position 4 is an amino acid selected from the group consisting of glycine or alanine, and (iv) the X at position 5 is an amino acid selected from the group consisting of asparagine, aspartic acid, alanine, or serine, and (v) the X at position 6 is an amino acid selected from the group consisting of aspartic acid or asparagine, (vi) the X at position 7 is an amino acid selected from the group consisting of threonine, isoleucine, valine, or leucine, and (vii) the X at position 8 is an amino acid selected from the group consisting of leucine, isoleucine, or phenylalanine, and (viii) the X at position 9 is an amino acid selected from the group consisting of tyrosine, isoleucine, valine, phenylalanine, threonine, asparagine, aspartic acid, lysine or serine, or (c) a variant PBRT, wherein the PBRC further comprises a cleavage site located N-terminally or C-terminally to one or more of the one or more PBRTs. In certain embodiments, the cleavage site is selected from the group comprising an intein cleavage site, a Factor Xa cleavage site, a thrombin cleavage site, an enterokinase cleavage site, or a signal peptidase cleavage site.
In certain aspects, the invention relates to a polypeptide comprising a PBRC linked purification moiety comprising a precipitable beta roll cassette (PBRC) comprising one or more beta roll tags (PBRTs) wherein the one or more PBRTs are independently any of: (a) a polypeptide having the amino acid sequence of SEQ ID NO: 1, or (b) a polypeptide having the amino acid sequence of any of SEQ ID NOs 25-1337, (c) a polypeptide comprising the amino acid sequence GXXXXXXXX (SEQ ID NO: 1343), wherein, (i) the X at position 2 is an amino acid selected from the group consisting of glycine, asparagine or aspartic acid, and (ii) the X at position 3 is an amino acid selected from the group consisting of alanine, serine, glycine, aspartic acid, glutamic acid, leucine or asparagine, and (iii) the X at position 4 is an amino acid selected from the group consisting of glycine or alanine, and (iv) the X at position 5 is an amino acid selected from the group consisting of asparagine, aspartic acid, alanine, or serine, and (v) the X at position 6 is an amino acid selected from the group consisting of aspartic acid or asparagine, (vi) the X at position 7 is an amino acid selected from the group consisting of threonine, isoleucine, valine, or leucine, and (vii) the X at position 8 is an amino acid selected from the group consisting of leucine, isoleucine, or phenylalanine, and (viii) the X at position 9 is an amino acid selected from the group consisting of tyrosine, isoleucine, valine, phenylalanine, threonine, asparagine, aspartic acid, lysine or serine, or (c) a variant PBRT; and a purification moiety.
In certain aspects, the invention relates to a nucleic acid encoding any of the polypeptides described herein.
In certain embodiments, the invention relates to a method for purifying a PBRC linked purification moiety, the method comprising (a) expressing the PBRC linked purification moiety in an expression system, (b) collecting the PBRC linked purification moiety in a first medium, (c) adding Ca2+ to the first medium so as to induce precipitation of PBRC linked purification moiety, (d) removing unprecipitated material from the medium from the precipitated PBRC linked purification moiety, (e) resuspending the PBRC linked purification moiety in a second medium having a lower than the free Ca2+ concentration than the free Ca2+ concentration obtained after step (c). In certain embodiments, a calcium chelator is added to the second medium of step (e). In certain embodiments, steps (c) to (e) are repeated one or more times. In certain embodiments, the method further comprises a step of removing precipitated material between step (b) and step (c). In certain embodiments, the PBRC comprises a cleavage site between the PBRC and the purification moiety. In certain embodiments, the method further comprises steps of: (i) cleaving the PBRC linked purification moiety so as to separate the purification moiety from the PBRC, (ii) adding Ca2+ to the medium so as to induce precipitation of the PBRC, and (iii) isolating the unprecipitated purification moiety. In certain embodiments, the cleavage site is an intein cleavage site.
In certain aspects, the invention relates to an expression vector comprising, as arranged from 5′ to 3′, a promoter, a nucleic acid sequence encoding the PBRC of any of claims 1-4, and at least one cloning site.
In certain aspects, the invention relates to an expression vector comprising, as arranged from 5′ to 3′, a promoter, at least one cloning site, and a nucleic acid sequence encoding the PBRC of any of claims 1-4.
In certain aspects, the invention relates to an expression vector comprising, as arranged from 5′ to 3′, a promoter, at least one cloning site, a nucleic acid sequence encoding the PBRC of any of claims 1-4 and at least a second cloning site.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1B show a SDS-PAGE gel showing purification of a molecule comprising a precipitable beta-roll tag. FIG. 1A shows purification of precipitatable maltose binding protein comprising a precipitatable beta roll tag and an enterokinase cleavage site (MBP-PBRT). Total lysate is shown in lane 1 and lanes 2-7 are precipitation/wash cycles. After two cycles, the sample consists nearly only of the MBP fusion protein with the precipitating tag attached (MBP-PBRT). Recovery is nearly 100% of the expressed protein. FIG. 1B shows SDS-PAGE analysis of purified MBP-PBRT and MBP-PBRT subjected to digestion of the enterokinase digestion site (FIG. 1B). Lane 1 shows purified MBP-PBRT, lane 2 shows supernatant after overnight digest and lane 3 shows the pellet.

FIG. 2 shows a SDS-PAGE gel showing a successful purification of a polypeptide comprising a 5 or 17 repeat C-capped precipitable beta-roll tags. Lanes (from left to right): 1. MBP-5cap lysate, 2. MBP-5cap supernatant, 3. MBP-5C resuspended precipitate. The 4-6 lanes are the same expect with the capped 17 repeat construct.

FIG. 3 is circular dichroism data (CD) showing precipitation of a polypeptide comprising a 17 repeat C-capped precipitable beta-roll tag (GGAGNDTLY)17INAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEII HAANQAVDQAGIEKLVEAMAQYPD (SEQ ID NO: 1344) out of solution with increasing calcium concentrations from 0 to 100 mM calcium. Loss of spectra indicates that the peptide is precipitating out of solution and no longer visible via CD.

FIG. 4 shows a GGXGXDXXX (SEQ ID NO: 2) sequence heat map. The heat map was determined by using BLAST to find beta roll sequences similar to the metalloprotease of S. marcescens and then quantifying the frequency of amino acids at each of the nine positions after beta roll sequences were identified. FIG. 4 discloses the consensus sequence as SEQ ID NO: 1343.

FIG. 5 shows a schematic illustration of the corkscrew configuration of tandem Ca2+ binding sequences. The figure shows a crystal structure image of the beta roll domain from the metalloprotease of S. marcescens (1SAT in the Protein Databank). Alternating 9-amino acid repeats are highlighted in green and red. Coordinated calcium ions are in white. The image represents 5 repeats of beta roll sequence. While there is no crystal structure for the adenylate cyclase beta roll domain, the high degree of sequence similarity to the consensus beta roll indicates that the adenylate cyclase beta roll domain is similar.

FIG. 6 shows a schematic illustration of the corkscrew configuration of tandem Ca2+ binding sequences from a different angle than shown in FIG. 5. The 6th residue binds the calcium ion. The 7th and 9th residues of each repeat are those that face outwards. The 8th residue is buried in the hydrophobic core. These residues are threonine and tyrosine, respectively in SEQ ID NO: 1.

FIG. 7 shows the full crystal structure of the metalloprotease of S. marcescens. The black spheres indicate the position of the calcium ions within the beta roll domain.

FIGS. 8A-8D show a characterization of beta roll distribution, sequence deviation and number of repeats. FIG. 8A shows a distribution of beta roll lengths as frequency plotted against the number of beta roll repeats. FIG. 8B shows beta roll sequence deviation from consensus by position plotted as proportion deviation as a function of distance from terminus FIG. 8C shows a probability of deviation from consensus plotted as probability as a function of the number of beta roll repeats. FIG. 8D shows amount of beta roll in overall protein plotted as the number of beta roll residues as a function of the number of total residues.

FIG. 9 shows an exemplary protocol for purification of a polypeptide comprising a precipitable beta roll tag. The images depict precipitation of maltose binding protein fused to seventeen repeats of a PBRT. The PBRC comprises 17 repeats of the amino acid sequence of SEQ ID NO: 1. The PBRC does not comprise a capping sequence.

FIG. 10 shows purification of a maltose binding protein/PBRT/green fluorescent protein fusion (MBP-PBRT-GFP). FIG. 10A shows a precipitation and resuspension of the MBP-PBRT-GFP polypeptide. FIG. 10B shows SDS-PAGE of multiple precipitation wash cycles. The lanes of the SDS gel are as follows: lane 1-ladder; lane 2-clarified lysate; lane 3-precipitation in 25 mM calcium followed by three washes; lane 4-precipitation in 50 mM calcium followed by three washes; lane 5-precipitation in 75 mM calcium followed by three washes; lane 6-precipitation in 100 mM calcium followed by three washes. All lanes are normalized in terms of concentration. Recovery percentage can be estimated by comparing the band intensity in lane 2 to subsequent lanes.

FIG. 11 shows non-limiting examples of polypeptides comprising a PBRT suitable for use with the methods described herein. FIG. 11 discloses SEQ ID NO: 1368.

FIGS. 12A-12G show vector Maps at shown in FIG. 12A-G. Vector maps are given for each construct prepared, highlighting the important features.

FIGS. 13A-13B show beta roll structure and sequence logo. FIG. 13A shows crystal structure of β roll domain from metalloprotease of S. marcescens (PDB: 1SAT). FIG. 13B shows amino acid frequencies for single β roll repeat identifying consensus sequence GGAGNDTLY (SEQ ID NO: 1). Height of the letter corresponds to proportion of sequences containing the particular amino acid at that position.

FIG. 14 shows the role of PBRT length in precipitation. Mass of precipitated pellet vs. calcium chloride concentration and PBRT size. Results for MBP-PBRT5(1), MBP-PBRT9(), MBP-PBRT13(◯), and MBP-PBRT17(▾). Error bars represent standard deviations for 3 trials.

FIG. 15 shows ion specificity of PBRT precipitation. Purified MBP-PBRT17-GFP was mixed with 100 mM of the compound indicated, and centrifuged to collect any pellet. The tube was then inverted so that precipitated protein remained on top. The compounds were as follows: (a) CaCl2, (b) MgCl2, (c) MnCl2, (d) NaCl, and (e) (NH4)2SO4

FIG. 16 shows SDS-PAGE results for purification of the four constructs tested. Numbers are standard size in kDa. Expected molecular weights for MBP-PBRT17, MBP-PBRT17-GFP, MBP-PBRT17-βlac, and MBP-PBRT17-AdhD are 57.1, 83.4, 88.6, and 89.1 kDa, respectively. (1-2) Purification of MBP-PBRT17. Lane 1 is clarified lysate, and Lane 2 is purified fusion protein. (3-4) Same samples for purification of MBP-PBRT17-GFP. (5-6) Same samples for MBP-PBRT17-βlac. (7-8) Same samples for MBP-PBRT17-AdhD.

FIG. 17 shows SDS-PAGE results for purification and cleavage of AdhD. Numbers are standard size in kDa. Estimated molecular weight for AdhD is 31.9 kDa. (1) Clarified MBP-PBRT17-AdhD lysate. (2) Purified fusion protein. (3) Enterokinase cleavage. (4) Precipitated MBP-PBRT17. (5) Soluble AdhD. 3× protein concentrations were used in

lanes

3, 4, and 5.

DESCRIPTION

The issued patents, applications, and other publications that are cited herein are hereby incorporated by reference to the same extent as if each was specifically and individually indicated to be incorporated by reference.
Purification is a major requirement in many bioengineering applications where significant amounts of time are currently spent purifying proteins from heterogeneous samples. The invention described herein relates to methods for rapidly purifying a purification moiety (e.g. a target polypeptide) from a heterogeneous medium using a PBRC. For example, in certain embodiments, a target polypeptide can be produced as a fusion protein in frame with a PBRC. In certain embodiments, the fusion protein comprising the target protein and the PBRC can further comprise a specific cleavage site (e.g. an intein cleavage site or an enterokinase cleavage site) between the target protein sequence and the PBRC sequence. In such embodiments, cleavage at the cleavage site can be used to separate the PBRC from the target polypeptide.
The beta-roll domain is a right-handed beta helix found in a number of proteins. The consensus sequence for beta-roll peptides is tandem repeats of the 9 amino acid sequence GGXGXDX(L/F/I)X (SEQ ID NO: 24). In the presence of calcium, the conformation aligns to adopt the helical turns. Two repeats of the sequence are required to make a complete helical turn and each of these turns binds a calcium atom. In the absence of calcium, the peptide exists in a disordered conformation. Therefore the β-roll domain exhibits natural allosteric regulation. A synthetic version of the β-roll peptide has been produced with 8 repeats of GGSGNDNLS (SEQ ID NO: 1338) and this peptide was found to bind calcium and fold into the β-roll structure (Lilie et al., FEBS Lett 470 (2), 173 (2000)). The domain is capable of reversibly unfolding upon removal of the calcium. Beta roll sequences are known to play a role in secretion as part of the bacterial Type I secretion system (Davidson, et al., Microbiol. Mol. Biol. Rev. 72 (2008), pp. 317-364; Holland et al., Mol. Membr. Biol. 22 (2005), pp. 29-39; Chenal, et al., J. Biol. Chem. 284 (2009), pp. 1781-1789; Welch, Pore-Forming Toxins 257 (2001), pp. 85-111; Rose et al., J. Biol. Chem. 270 (1995), pp. 26370-26376; Baumann, J. Mol. Biol. 242 (1994), pp. 244-251; Angkawidjaja, et al., FEBS Lett. 581 (2007), pp. 5060-5064; Meier et al., J. Biol. Chem. 282 (2007), pp. 31477-31483; Bauche et al., J. Biol. Chem. 281 (2006), pp. 16914-16926; Baumann et al., EMBO J. 12 (1993), pp. 3357-3364; Angkawidjaja et al., FEBS Lett. 579 (2005), pp. 4707-4712).
The precipitable-beta roll tags and precipitable-beta roll cassettes described herein are class of designed peptides which possess the ability to reversibly precipitate in response to calcium ions. In one aspect, the invention described herein relates to the surprising finding that PBRCs (e.g. PBRTs repeats of sequence GGAGNDTLY (SEQ ID NO: 1)) undergo reversible precipitation upon calcium binding. In another aspect, the invention described herein relates to the surprising finding that attachment of a PBRC to a second molecule (e.g. attachment to a protein as a fusion protein comprising an in-frame) can be used to purify the second molecule through reversible precipitation. In another aspect, the invention described herein relates to the use of calcium concentration changes at room temperature to induce precipitation of recombinant molecules comprising a precipitable beta-roll tag.
In addition to target polypeptides, the PBRCs describe herein are also suitable for purifying non-peptide purification moieties of widely varying types, including, for example, lipids, oligonucleotides and carbohydrates, small organic or inorganic molecules, proteins, single-stranded or double-stranded oligonucleotides, polynucleotides. In certain aspects, applications for the methods and compositions described herein include, but are not limited to, the purification of recombinant proteins the removal of target proteins from a sample, and detection of compounds for diagnostic purposes. The invention also extends to the antibodies that specifically bind to a PBRT or a PBRC and the methods for using the PBRTs and PBRCs described herein.
Without wishing to be bound to theory, in certain embodiments, the PBRTs and PBRCs described herein can undergo a reversible Ca2+ binding dependent transition wherein they are structurally disordered and highly soluble in a medium below a Ca2+ concentration (or free Ca2+) transition concentration, but exhibit a disorder to order phase transition when the Ca2+ or free Ca2+ concentration is raised above the Ca2+ (or free Ca2+) transition concentration. Again, without wishing to be bound by theory, in some embodiments, the disorder to order phase transition leads to precipitation of the PBRTs or PBRCs. Precipitation of PBRC can be used to remove and isolated them from solution (e.g. by centrifugation). In one embodiment, the invention described herein relates to a PBRC which functions reversible Ca2+ precipitable tag when linked to a purification moiety of interest. In embodiments where the PBRC is linked to a purification moiety of interest, the methods described herein can be used to induce precipitation of the PBRC linked purification moiety. Because the transition concentration dependent phase transition is reversible, the PBRT and PBRC can be resolubilized in a medium having a Ca2+ concentration (or free Ca2+) below the transition concentration. In certain embodiments, this can be accomplished by introducing medium having reduced, or no Ca2+, or by removing, or chelating Ca2+ from the medium. When the precipitate is resuspended in calcium-free buffer or in a buffer comprising a calcium ion chelator (e.g. EGTA or EDTA), the precipitate resuspends into solution.
The singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise.
The term “about” is used herein to mean approximately, in the region of, roughly, or around. When the term “about” is used in conjunction with a numerical range, it modifies that range by extending the boundaries above and below the numerical values set forth. In general, the term “about” is used herein to modify a numerical value above and below the stated value by a variance of 20%.
In certain embodiments, the term “precipitable-beta roll tag” (PBRT) refers to an amino acid sequence having the sequence GGAGNDTLY (SEQ ID NO: 1). In certain embodiments, a PBRT refers to an amino acid sequence having the amino acid sequence GXXXXXXXX (SEQ ID NO: 1343), wherein (a) the X at position 2 is an amino acid selected from the group consisting of glycine, asparagine or aspartic acid, and (b) the X at position 3 is an amino acid selected from the group consisting of alanine, serine, glycine, aspartic acid, glutamic acid, leucine or asparagine, and (c) the X at position 4 is an amino acid selected from the group consisting of glycine or alanine, and (d) the X at position 5 is an amino acid selected from the group consisting of asparagine, aspartic acid, alanine, or serine, and (e) the X at position 6 is an amino acid selected from the group consisting of aspartic acid or asparagine, (f) the X at position 7 is an amino acid selected from the group consisting of threonine, isoleucine, valine, or leucine, and (g) the X at position 8 is an amino acid selected from the group consisting of leucine, isoleucine, or phenylalanine, and (h) the X at position 9 is an amino acid selected from the group consisting of tyrosine, isoleucine, valine, phenylalanine, threonine, asparagine, aspartic acid, lysine or serine, or a nucleic acid encoding the same. A PBRT refers to an amino acid sequence having the sequence set forth in any of SEQ ID NOs: 25-1337.
As used herein, the term “precipitable-beta roll cassette” (PBRC) refers to an amino acid sequence comprising at least one PBRT. In certain embodiments, a PBRC will comprise at least two PBRTs. In certain embodiments, a PBRC will comprise at least 3 PBRTs, at least 4 PBRTs, at least 5 PBRTs, at least 6 PBRTs, at least 7 PBRTs, at least 8 PBRTs, at least 9 PBRTs, at least 10 PBRTs, at least 11 PBRTs, at least 12 PBRTs, at least 13 PBRTs, at least 14 PBRTs, at least 15 PBRTs, at least 16 PBRTs, at least 17 PBRTs, at least 18 PBRTs, at least 19 PBRTs, at least 20 PBRTs, or 20 or more PBRTs. In certain embodiments, the PBRCs described herein will comprise a plurality of precipitable beta roll tags arranged in a tandem repeat. For example, in certain embodiments, the PBRCs described herein can comprise at least 2 PBRTs, at least 3 PBRTs, at least 4 PBRTs, at least 5 PBRTs, at least 6 PBRTs, at least 7 PBRTs, at least 8 PBRTs, at least 9 PBRTs, at least 10 PBRTs, at least 11 PBRTs, at least 12 PBRTs, at least 13 PBRTs, at least 14 PBRTs, at least 15 PBRTs, at least 16 PBRTs, at least 17 PBRTs, at least 18 PBRTs, at least 19 PBRTs, at least 20 PBRTs, or 20 or more PBRTs in tandem repeat. In certain embodiments, a PBRC can comprise at least two PBRCs separated by a linking amino acid sequence. Where a linking amino acid sequence in present between two PBRTs, a PBRT located at either end of the linking sequence can be an individual PBRT or it can be a PBRT that is part of a tandem arrangement of two or more PBRTs.
The PBRCs can comprise polymeric or oligomeric repeats of a PBRT. In certain embodiments, the PBRCs described herein can comprise one or more different PBRTs. In one embodiment, all of the PBRTs comprised in a PBRC are identical in amino acid sequence. In one embodiment, all of the PBRTs comprised in a PBRC have different amino acid sequences. In one embodiment, at least one PBRT comprised in a PBRC has a different amino acid sequence as compared to another PBRT in the PBRC. Thus, in certain embodiments, the PBRCs described herein can comprise at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 different PBRTs.
In certain embodiments, a PBRC can also comprise a capping sequence (“CS”) refers to the an amino acid sequence comprising the amino acid sequence of SEQ ID NO: 3. The term “capping sequence” also refers to a capping sequence having the amino acid sequence of any of SEQ ID NO: 4-23.
Without wishing to be bound to theory, in some embodiments of the invention, the ability of polypeptide comprising one or more PBRT to undergo reversible Ca2+ precipitation, can require that the one or more PBRTs be located N-terminally or C-terminally to a capping sequence. Thus, in certain embodiments, the capping sequence is an amino acid sequence, which, when located C-terminally or N-terminally to one or more PBRTs, allows the one or more PBRTs bind to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the PBRC.
Thus in certain embodiments, a PBRC will comprise at least 2 PBRTs, at least 3 PBRTs, at least 4 PBRTs, at least 5 PBRTs, at least 6 PBRTs, at least 7 PBRTs, at least 8 PBRTs, at least 9 PBRTs, at least 10 PBRTs, at least 11 PBRTs, at least 12 PBRTs, at least 13 PBRTs, at least 14 PBRTs, at least 15 PBRTs, at least 16 PBRTs, at least 17 PBRTs, at least 18 PBRTs, at least 19 PBRTs, at least 20 PBRTs, or 20 or more PBRTs, all of which are located N-terminally to a CS. In certain embodiments, a PBRC will comprise 2, at least 3 PBRTs, at least 4 PBRTs, at least 5 PBRTs, at least 6 PBRTs, at least 7 PBRTs, at least 8 PBRTs, at least 9 PBRTs, at least 10 PBRTs, at least 11 PBRTs, at least 12 PBRTs, at least 13 PBRTs, at least 14 PBRTs, at least 15 PBRTs, at least 16 PBRTs, at least 17 PBRTs, at least 18 PBRTs, at least 19 PBRTs, at least 20 PBRTs, or 20 or more PBRTs, all of which are located C-terminally to a CS.
In one embodiment, a PBRC is an amino acid sequence comprising at least five tandem PBRTs situated N-terminally to a capping sequence.
In one embodiment, a PBRC is an amino acid sequence comprising at least six to about 16 tandem PBRTs situated N-terminally to a capping sequence.
In one embodiment, a precipitable beta roll cassette is an amino acid sequence comprising 17 or more tandem PBRTs situated N-terminally to a capping sequence.
In one embodiment, the capping sequence comprises the sequence INAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGI EKLVEAMAQYPD (SEQ ID NO: 3) which is a C-terminal sequence on the block V beta roll domain of the adenylate cyclase toxin of B. pertussis.
In another embodiment, a PBRC comprises the amino acid sequence GGAGNDTLYGGAGNDTLYGGAGNDTLYGGAGNDTLYGGAGNDTLYINAGADQLW FARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGIEKLVEAMAQ YPD (SEQ ID NO: 4). In another embodiment, a PBRC comprises the amino acid sequence GGAGNDTLYGGAGNDTLYGGAGNDTLYGGAGNDTLYGGAGNDTLYGGAGNDTL YGGAGNDTLYGGAGNDTLYGGAGNDTLYGGAGNDTLYGGAGNDTLYGGAGNDT LYGGAGNDTLYGGAGNDTLYGGAGNDTLYGGAGNDTLYGGAGNDTLYINAGADQ LWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGIEKLVEAM AQYPD (SEQ ID NO: 5). In another embodiment, the capping sequence comprises the sequence INAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEAIHAANQAIDPAGI EKLVEAMAQYPD (SEQ ID NO: 6) (adenylate cyclase-hemolysin [Bordetella bronchiseptica]). In another embodiment, the capping sequence comprises the sequence INAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEAIHAANQAIDPAGI EKLVEAMAQYPD (SEQ ID NO: 7) (adenylate cyclase-hemolysin [Bordetella bronchiseptica]). In another embodiment, the capping sequence comprises the sequence INAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEAIHAANQTVDPAGI EKLVEAMAQYPD (SEQ ID NO: 8) (adenylate cyclase hemolysin [Bordetella bronchiseptica]). In another embodiment, the capping sequence comprises the sequence QLWFSKSGSDLEVRVVGTDDAVTVAGWYSGAEHHMDSIETADGTVLLDSMVDRLV QAMAGF (SEQ ID NO: 9) (Azospirillum sp. B510 calcium binding hemolysin protein). In another embodiment, the capping sequence comprises the sequence ADQLWFRHVGNDLEISILGTGDTATVRDWYLGSRYQIEQIRVDDGRTLVNADVEKL VQAMA (SEQ ID NO: 10) (hemolysin-type calcium-binding region Burkholderia cenocepacia MCO-3). In another embodiment, the capping sequence comprises the sequence ADQLWFRHVGNDLEISILGSSDTATVRDWYSGSRYQIEQIRLDDGRTLVNADVEKLV QAMA (SEQ ID NO: 11) (hemolysin-type calcium-binding region [Burkholderia ambifaria MC40-6]). In another embodiment, the capping sequence comprises the sequence DARQTNLWFSQVGKDLQIDVLGSTDQVTVKDWYAGADNRVERIKTADGKTLYDSD VDKLVQAMASF (SEQ ID NO: 12) (calcium binding secreted hemolysin protein)[Herbaspirillum seropedicae SmR1]). In another embodiment, the capping sequence comprises the sequence DARQTNLWFSQVGKDLQIDVLGSTDQVTVKDWYAGADNRVERIKTADGKTLYDSD VDKLVQAMASF (SEQ ID NO: 13) (calcium binding secreted hemolysin protein [Herbaspirillum seropedicae SmR1]). In another embodiment, the capping sequence comprises the sequence ELWFSRENNDLIIKSLLSEDKVTVQNWYSHQDHKIENIRLSNEQTLVSTQVEKMVES MAGF (SEQ ID NO: 14) (RTX toxin protein [Actinobacillus pleuropneumoniae serovar). In another embodiment, the capping sequence comprises the sequence EELWFSRDGNDLQINVIGTDNQVEISDWYSGVNYQLDKVQVGDSVLLNTQLEQLVS AMASF (SEQ ID NO: 15) (hemolysin-type calcium binding protein [Shewanella piezotolerans WP3]). In another embodiment, the capping sequence comprises the sequence GLSELWFSRENNDLIIKSLLSEDKVTVQNWYSHQDHKIENIRLSNEQMLVSTQVEKM VESMAGF (SEQ ID NO: 16) (RTX toxin protein [Actinobacillus pleuropneumoniae serovar 10). In another embodiment, the capping sequence comprises the sequence EDLWFSRDGNNLQINIIGTDDQVEVNNWYNDTNYQLDQIQVGGSVLLNNQLEQLVS AMASF (SEQ ID NO: 17) (RTX toxin [Shewanella violacea D5512]). In another embodiment, the capping sequence comprises the sequence ELWFSRENNDLIIKSLLSEDKVTVQNWYSHQDHKIENIRLSNEQTLVSTQVEKMVES MASF (SEQ ID NO: 18) (RTX toxin protein [Actinobacillus pleuropneumoniae serovar 6). In another embodiment, the capping sequence comprises the sequence ADNFWFVKSGNDLEIDILGTHQQVTVADWFLGGSYQLQEIKAGGLELDTQVTQLVQ AMATY (SEQ ID NO: 19) (protein BRAD06535 [Bradyrhizobium sp. OR5278]). In another embodiment, the capping sequence comprises the sequence ELWFSRENNDLIIKSLLSEDKVTVQNWYSHQDHKIENIRLSNEQTLVSTQVEKMVES MAGF (SEQ ID NO: 20) ([Actinobacillus pleuropneumoniae L20]). In another embodiment, the capping sequence comprises the sequence LWFSRENNDLIIKSLLSEDKVTVQNWYSHQDHKIENIRLSNEQTLVSTQVEKMVESM AGF (SEQ ID NO: 21) (ApxIVA [Actinobacillus pleuropneumoniae]). In another embodiment, the capping sequence comprises the sequence LWFRKSGNNLEVSIIGTSDKLVMSNWYAGSQYQVERFQAGDGKALQANQVQSLVQ AMASF (SEQ ID NO: 22) (hemolysin-type calcium-binding protein [Xanthomonas axonopodis pv. citri str. 306]). In another embodiment, the capping sequence comprises the sequence ELWFSRENNDLIIKSLLSEDKVTVQNWYSHQDHKIENIRLSNEQTLVSTQVEKMVES MAGF (SEQ ID NO: 23) (RTX toxin WA [Actinobacillus pleuropneumoniae])
Without wishing to be bound to theory, in some embodiments of the invention, the ability of polypeptide comprising one or more PBRT to undergo reversible Ca2+ precipitation, can require that the one or more PBRTs be located N-terminally or C-terminally to a stabilizing polypeptide. It is known that when a certain stabilizing polypeptides (e.g. GFP, maltose binding protein) are attached to the C-terminus of the beta roll, calcium-induced folding can occur (Blenner et al., Journal of Molecular Biology. 400 (2010), pp 244-256; Szilvay et al., Biochemistry, 48 (2009), pp 11273-11282).
Thus, in one embodiment, a PBRC is an amino acid sequence comprising one or more PBRTs located N-terminally or C-terminally to a stabilizing polypeptide, wherein the stabilizing polypeptide cane be, but is not limited to, glutathione S-transferase (GST), maltose E binding protein (MBP), Green Fluorescent Protein (GFP), and variants thereof. In still a further embodiment, the stabilizing polypeptide is an amino acid sequence of any amino acid composition wherein the sequence comprises at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46, at least 47, at least 48, at least 49, at least 50, at least 51, at least 52, at least 53, at least 54, at least 55, at least 56, at least 57, at least 58, at least 59, at least 60, at least 61, at least 62, at least 63, at least 64, at least 65, at least 66, at least 67, or at least 68 amino acids.
In another aspect of the invention, the PBRCs described herein can further comprise one or more cleavage sites. In certain embodiments, the cleavage site can be positioned C-terminally or N-terminally to a PBRC so as to allow for cleavage of a PBRC from a linked purification moiety (e.g. a polypeptide purification moiety linked to a PBRC as part of a fusion protein). In embodiments where the PBRC comprises more than one cleavage site, a first cleavage site can be positioned C-terminally or N-terminally to a PBRC so as to allow for cleavage of a PBRC from a linked purification moiety (e.g. a polypeptide purification moiety linked to a PBRC as part of a fusion protein) and a second cleavage site can be positioned between a PBRT and a capping sequence or a PBRT and a stabilizing polypeptide so as to allow so as to allow for cleavage of the capping sequence or the stabilizing polypeptide from the one or more PBRTs in the PBRC. In certain embodiments, cleavage at such cleavage sites can be useful for purification of a purification moiety of interest.
In one embodiment, the cleavage site is a proteolytic cleavage site. Exemplary proteolytic cleavage sites, include, but are not limited to Factor Xa, thrombin, or enterokinase. In another embodiment, the cleavage site is a signal peptidase cleavage site. In another embodiment, the cleavage site is a self cleaving intein cleavage site (Amitai et al., Proceedings of the National Academy of Sciences, vol. 106, no. 27, pp. 11005-11010, July 2009; Hiraga et al., Journal of Molecular Biology, vol. 393, no. 5, pp. 1106-1117, November 2009). Any other specific cleavage sites known in the art can be used in connection with the methods described herein.
The PBRTs or PBRCs described herein may be linked to a purification moiety by any means known in the art. The PBRTs or PBRCs described herein can be located at any site in a polypeptide comprising a purification moiety of interest, including a location that is N-terminal, a location that is C-terminal or a location within the sequence of the purification moiety of interest.
In addition to fusion proteins comprising the PBRTs or PBRCs described herein, the PBRTs or PBRCs described herein can also be chemically linked to purification moieties other than by means of a fusion protein. Thus, reference to a PBRC linked purification moiety, or to a PBRT linked purification moiety encompasses for purification moieties linked to a PBRC or PBRT by peptide linkage (e.g. as a fusion protein) or by non-peptide bond chemical linkage.
The chemical modification of PBRTs or PBRCs described herein can be performed according to any method known in the art. For example, amides of the PBRTs or PBRCs described herein can be prepared by techniques well known in the art for converting a carboxylic acid group or precursor, to an amide. One method for amide formation at the C-terminal carboxyl group is to cleave the polypeptide, or fusion thereof from a solid support with an appropriate amine, or to cleave in the presence of an alcohol, yielding an ester, followed by aminolysis with the desired amine.
Salts of carboxyl groups of the PBRTs or PBRCs described herein can be prepared by contacting the polypeptide, or fusion thereof with one or more equivalents of a desired base such as, for example, a metallic hydroxide base, e.g., sodium hydroxide; a metal carbonate or bicarbonate base such as, for example, sodium carbonate or sodium bicarbonate; or an amine base such as, for example, triethylamine, triethanolamine, and the like.
N-acyl derivatives of an amino group of the PBRTs or PBRCs described herein can be prepared by utilizing an N-acyl protected amino acid for the final condensation, or by acylating a protected or unprotected polypeptide, or fusion thereof O-acyl derivatives can be prepared, for example, by acylation of a free hydroxy polypeptide or polypeptide resin. Either acylation can be carried out using standard acylating reagents such as acyl halides, anhydrides, acyl imidazoles, and the like. Both N- and O-acylation can be carried out together, if desired.
Formyl-methionine, pyroglutamine and trimethyl-alanine can be substituted at the N-terminal residue of PBRTs or PBRCs described herein. Other amino-terminal modifications include aminooxypentane modifications.
Such chemical linkages can be useful for purifying non-peptide molecules such as lipids, oligonucleotides and carbohydrates, small organic or inorganic molecules, proteins, single-stranded or double-stranded oligonucleotides, polynucleotides, metals (e.g. cobalt, zinc, nickel or copper) and the like. The chemically modified PBRTs or PBRCs described herein can be assayed for the ability to bind to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the PBRT or PBRC using methods known to those skilled in the art.
The PBRTs and PBRCs described herein can also be coupled with a radioisotope or enzymatic label to facilitate their detection. For example, the PBRTs or PBRCs described herein can be isotopically-labeled where one or more atoms are replaced or substituted by an atom having an atomic mass or mass number different from the atomic mass or mass number typically found in nature (i.e., naturally occurring). Suitable radionuclides that may be incorporated in compounds of the present invention include but are not limited to ²H (also written as D for deuterium), ³H (also written as T for tritium), ¹¹C, ¹³C, ¹⁴C, ¹³N, ¹⁵N, ¹⁵O, ¹⁷O, ¹⁸O, ¹⁸F, ³⁵S, ³⁶Cl, ⁸²Br, ⁷⁵br, ⁷⁶Br, ⁷⁷Br, ¹²³I, ¹²⁴I, ¹²⁵I and ¹³¹I. The radionuclide that is incorporated in the instant radio-labeled compounds can depend on the specific application of that radio-labeled compound.
Alternatively, the PBRTs or PBRCs described herein can be enzymatically labeled with, for example, horseradish peroxidase, alkaline phosphatase, or luciferase, and the enzymatic label detected by determination of conversion of an appropriate substrate to product. In another embodiment, the PBRTs or PBRCs described herein can be labeled with a fluorescent dye, spin label, heavy metal or radio-labeled peptides.
Esters of carboxyl groups of the PBRTs or PBRCs described herein can also be prepared by any of the usual methods known in the art.
The methods and compositions described herein are useful in a broad range of bioseparation applications. The methods and compositions described herein can be used for rapid expression and purification of a purification moiety linked to a PBRC. Such PBRC linked purification moieties can be expressed in any number of expression systems, including in vitro and in vivo expression systems. Exemplary in vivo expression systems suitable for expressing the PBRC linked purification moieties described herein, include, but are not limited to, bacterial systems, yeast systems, and mammalian systems.
In one aspect, the invention relates to a method for purifying purification moieties (e.g. a PBRC or a purification moiety linked to a PBRC). In one aspect, the methods described herein can be used for purifying one or more purification moieties from a heterogeneous mixture of biomaterials in a sample. In another aspect, the methods descried herein can be used to purify chemically synthesized purification moieties or in-vitro synthesized purification moieties.
In certain embodiments, the bioseparation methods described herein can comprise expressing a PBRT linked purification moiety (e.g. a PBRC fusion protein) in a cellular expression system (e.g. a bacterial cell). The PBRC linked purification moiety can then be released into a medium by cell lysis. Any method of cell lysis known in the art can be used in conjunction with the methods described herein, including, but not limited to chemical lysis (e.g. detergents) or physical methods (e.g. sonication or French press). In certain embodiments, the PBRC or PBRC linked purification moiety can be expressed in an in-vitro expression system (e.g. a rabbit reticulocyte system) such that the purification moiety is expressed into the expression system medium.
After expression of the PBRC linked purification moiety, bioseparation can be achieved by increasing the free Ca2+ concentration in the medium comprising the PBRC linked purification moiety to induce precipitation of the PBRC linked purification moiety, followed by removing material that does not precipitate from the medium and then resuspending the precipitated material in a medium having a reduced Ca2+ concentration or in a medium having a reduced concentration of free Ca2+ (e.g. a medium comprising a Ca2+ chelators such as EDTA). These steps can be repeated until the desired level of purity is reached.
In another embodiment, the PBRC linked purification moiety can be expressed in a cellular expression system, and bioseparation can be achieved by increasing the free Ca2+ concentration within the cell prior to cellular lysis. Many methods for increasing intracellular Ca2+ concentrations are known in the art, including, but not limited to adding Ca2+ to a cellular medium, with or without presence of ionophores or cell permeabilization agents. In such embodiments, the cells can then be subjected to lysis conditions (e.g. chemical lysis or physical lysis) and the resulting precipitate can be recovered. Precipitated PBRC or the PBRC linked purification moieties can then be recovered by reducing the free Ca2+ concentration (e.g. through the addition of a Ca2+ chelator) to induce solubilization of the purification moieties from the precipitate and bioseparation can be achieved by eliminating the precipitate. Precipitation and solubilization steps can be repeated until a desired level of purity is reached.
In still other embodiments, the PBRC linked purification moieties described herein can further comprise a peptide sequence to induce secretion into the periplasm of a cell (e.g. an E. coli cell) or to the medium outside of a cell. Where the PBRC linked purification moiety is secreted to the periplasm of a cell, cell lysis may be required for further purification of the PBRC linked purification moiety. Where the PBRC linked purification moiety is secreted into the medium outside of the cell, purification can be achieved without cell lysis by eliminating intact cells (e.g. by centrifugation) and purification of the PBRC linked purification moiety from the extracellular medium by increasing the free Ca2+ concentration of the supernatant.
The adjustment of conditions during the purification process can be achieved by numerous methods, including, but not limited to, adjusting the temperature, pH or salt concentration of the aqueous media.
The methods described herein can be used to purify purification moieties of any size. A purified PBRT linked purification moiety can contain less than about 50%, less than about 75%, or less than about 90%, of the materials with which it was originally associated.
In one embodiment, a purification moiety of interest can be linked to PBRC comprising a cleavable peptide sequence (e.g. a self-cleaving peptide sequence such an intein) positioned between the PBRC and the purification moiety. Once the PBRC linked purification moiety is expressed in an expression system, the PBRC linked purification moiety can be recovered using standard techniques as either a homogenous mixture or as a heterogeneous sample. The mixture can then be exposed to calcium to induce precipitation of the PBRC linked purification moiety. The PBRC linked purification moiety can then be resuspended in buffer that has reduced Ca2+, that has reduced free Ca2+ or that contains a calcium chelator (e.g. EDTA). The PBRC linked purification moiety can then be subjected condition that cause cleavage to separate the PBRC from the purification moiety and calcium can be once again added to the mixture. This will precipitate out the PBRC moiety and thereby leaving behind a sample of purified purification moiety of interest.
In another embodiment, PBRC linked purification moiety can be a moiety which binds a second molecule and the second molecule can be used to remove the purification moiety from the sample (e.g. a resin or beads coated with the second molecule) after induced cleavage at a site between the purification moiety and the PBRC.
In some embodiments, immobilization of the PBRC linked purification moieties described herein or its binding proteins can be used to facilitate separation of complexes from uncomplexed forms of one or both of the proteins, as well as to accommodate automation of the assay. Immobilization of the PBRC linked purification moieties described herein can be by linking to a solid support, including a plastic or glass plate or bead, a chromatographic resin, a filter or a membrane. Methods of attachment of proteins, or membranes containing same, to such supports are well known in the art. Immobilization of the PBRC linked purification moieties described herein can also be accomplished in any vessel suitable for containing the reactants. Examples include microtiter plates, test tubes, and micro-centrifuge tubes.
In one embodiment, a fusion protein can be provided which adds a domain that allows the PBRT linked purification moiety described herein to be bound to a matrix. For example, glutathione-S-transferase fusion proteins can be adsorbed onto glutathione sepharose beads or glutathione derivatized microtiter plates, which are then combined with the cell lysates, and the mixture incubated under conditions conducive to complex formation. Following incubation, the beads can be washed to remove any unbound fraction. Alternatively, the complexes can be dissociated from the matrix using standard electrophoretic techniques.
The methods described herein depend, in part on the finding that PBRCs undergo a reversible Ca2+ binding dependent transition. PBRCs or PBRC linked purification moieties undergo reversible precipitation at a Ca2+ concentration (or free Ca2+) phase transition concentration.
The transition concentrations reversible and the isolated precipitable beta-roll tags or purification moieties comprising a precipitable beta-roll tag can be completely resolubilized in a medium below a certain Ca2+ concentration (or free Ca2+) transition concentration, through, for example the addition of a calcium chelator into the medium comprising the PBRC or PBRC linked purification moiety.
The concentration of Ca2+ required to induce reversible precipitation of a PBRC or PBRC linked purification moiety can be readily determined by adding increasing amounts of Ca2+ until such time as the PBRC or PBRC linked purification moiety begins to precipitate from a the medium. One can readily determine the extent of precipitation by centrifuging the medium. In one embodiment, the amount of Ca2+ required to induce reversible precipitation a PBRC of PBRC linked purification moiety will be about 1 mM Ca2+, more than about 1 mM Ca2+, more than about 5 mM Ca2+, more than about 10 mM Ca2+, more than about 20 mM Ca2+, more than about 30 mM Ca2+, more than about 50 mM Ca2+, more than about 75 mM Ca2+, more than about 100 mM Ca2+, more than about 150 mM Ca2+, more than about 200 mM Ca2+, or more than about 500 mM Ca2+. In certain embodiments, the amount of Ca2+ required to induce precipitation of a PBRC or a PBRC linked purification moiety can increase as a function of the number of PBRTs in the PBRC. For example, a PBRC linked purification moiety comprising 8 PBRTs may precipitate in 150 mM Ca2+ wherein a PBRC linked purification moiety comprising 17 PBRTs may precipitate in 25 mM Ca2+. One of skill in the art will readily be capable of determining the amount of Ca2+ required to precipitate a particular PBRC or a particular PBRC linked purification moiety simply by titrating increasing concentrations of Ca2+.
The concentration of Ca2+ required to reverse precipitation of a PBRT or PBRC or of a PBRT or PBRC linked purification moiety can be readily determined by reducing the concentration of free Ca2+ in a medium until such time as a precipitated PBRC or PBRC linked purification moiety begins to solubilize into the medium. One can readily determine the extent of precipitation by centrifuging the medium. In one embodiment, the amount of free Ca2+ in the medium required to solubilize a precipitated PBRT or PBRC or of a PBRT or PBRC linked purification moiety will be less than about 1 mM Ca2+, less than about 1 mM Ca2+, less than about 5 mM Ca2+, less than about 10 mM Ca2+, less than about 20 mM Ca2+, less than about 30 mM Ca2+, less than about 50 mM Ca2+, less than about 75 mM Ca2+, less than about 100 mM Ca2+, less than about 150 mM Ca2+, less than about 200 mM Ca2+, or less than about 500 mM Ca2+. In certain embodiments, the free Ca2+ concentration required to reverse precipitation of a PBRC or a PBRC linked purification moiety can correlated to the number of PBRTs in the PBRC. For example, a PBRC linked purification moiety comprising 8 PBRTs may become soluble in a higher free Ca2+ concentration as compared to a PBRC linked purification moiety comprising 17 PBRTs. One of skill in the art will readily be capable of determining the Ca2+ concentration required to reverse precipitation a particular PBRC or a particular PBRC linked purification moiety simply by decreasing free Ca2+ concentrations.
The free Ca2+ concentration of a medium comprising a PBRC or a PBRC linked purification moiety can be reduced by adding one or more calcium chelators into the medium. Any number of calcium chelators can be used in the connection with the methods described herein. Examples of suitable calcium chelators include, but are not limited to EDTA, EGTA, and BAPTA. In one embodiment, the amount of a calcium chelator required to solubilize a precipitated PBRT or PBRC or of a PBRT or PBRC linked purification moiety will be about 1 mM Ca2+, more than about 1 mM Ca2+, more than about 5 mM Ca2+, more than about 10 mM Ca2+, more than about 20 mM Ca2+, more than about 30 mM Ca2+, more than about 50 mM Ca2+, more than about 75 mM Ca2+, more than about 100 mM Ca2+, more than about 150 mM Ca2+, more than about 200 mM Ca2+, or more than about 500 mM Ca2+.
In addition to temperature and ionic strength, other environmental variables useful for modulating the solubility of PBRT or PBRC or of the PBRT linked purification moieties described herein include pH, the addition of organic solutes and solvents, side-chain ionization or chemical modification, and pressure.
The PBRC linked purification moieties described herein can be further purified or isolated according to any method of protein purification or isolation known in the art. For example, PBRCs or PBRC linked purification moieties can be purified by various methods including, without limitation, preparative disc-gel electrophoresis, isoelectric focusing, HPLC, reversed-phase HPLC, gel filtration, ion exchange and partition chromatography, precipitation and salting-out chromatography, extraction, and countercurrent distribution. For some purposes, the PBRCs or the PBRC linked purification moieties can be produced in a recombinant system in which the protein contains an additional sequence tag that facilitates purification, such as, but not limited to, a polyhistidine sequence, or a sequence that specifically binds to an antibody, such as FLAG and GST. In one embodiment, the PBRCs or the PBRC linked purification moieties can be purified from a crude lysate of the host cell by chromatography on an appropriate solid-phase matrix. Alternatively, antibodies produced against the PBRTs or PBRCs, or a PBRC linked purification moiety or against polypeptides derived therefrom can be used as purification reagents.
The methods and compositions described herein can be useful for the detection of a broad range of purification moieties in biosensing applications. For example, the methods and compositions described herein can be used for the separation of protein of interest from a sample for detection of bimolecular interactions. In one embodiment, if a PBRC is linked to an antibody, the PBRC linked antibody can be added to a sample. Ca2+ can then be added to the sample to induce precipitation of the antibody such that antigen that interact with, or form a complex with, the antibody also precipitate upon the addition of Ca2+. The precipitate can then be collected and resuspended and the sample can be characterized. The presence and quantity of the target in the original sample, as well as any associated purification moieties, can be characterized and determined. Any antibodies, antibody fragments, antibody configurations, classes, or subclasses known in the art can be used in connection with the methods described herein. In another embodiment, if a PBRC is fused to a polypeptide capable of binding to a second purification moiety, it can be added to a sample. Ca2+ can then be added to the sample to induce precipitation of the polypeptide such that other purification moieties that interact with, or form a complex with, the polypeptide also precipitate upon the addition of Ca2+. The precipitate can then be collected and resuspended and the sample can be characterized. The presence and quantity of the target in the original sample, as well as any associated additional purification moieties, can be characterized and determined.
The PBRC linked purification moieties described herein can be produced in prokaryotic or eukaryotic host cells by expression of nucleic acids encoding a polypeptide of this invention. The production of these polypeptides can also be done as part of a larger polypeptide.
The PBRC linked purification moieties described herein can also be synthesized in vitro, e.g., by the solid phase polypeptide synthetic method or by recombinant DNA approaches described herein. The solid phase polypeptide synthetic method is an established and widely used method. These PBRC or PBRC linked purification moieties described herein can be further purified by fractionation on immunoaffinity or ion-exchange columns; ethanol precipitation; reverse phase HPLC; chromatography on silica or on an anion-exchange resin such as DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; gel filtration using, for example, Sephadex G-75; or ligand affinity chromatography.
The PBRC linked purification moieties described herein can also be produced using any in-vitro expression system known in the art or can be synthesized by chemical methods. Methods for expression of heterologous proteins in recombinant hosts, chemical synthesis of polypeptides, and in vitro translation are well known in the art and are described further in Sambrook J et al.; Berger and Kimmel, Methods in Enzymology, Volume 152, Guide to Molecular Cloning Techniques (1987), Academic Press, Inc., San Diego, Calif.; Gutte B and Merrifield R B, J. Am. Chem. Soc. 91:501-02 (1969); Chaiken I M, CRC Crit. Rev. Biochem. 11:255-301 (1981); Kaiser E T et al., Science 243:187-92 (1989); Merrifield B, Science 232:341-47 (1986); Kent S B H, Ann. Rev. Biochem. 57:957-89 (1988); Offord, R. E. (1980) Semisynthetic Proteins, Wiley Publishing. Exemplary peptide synthesis methods known in the art include, but are not limited to those described in Stewart et al., Solid Phase Peptide Synthesis, Pierce Biotechnology, Inc., Rockford, Ill., 1984; Bodanszky, Principles of Peptide Synthesis, Springer-Verlag, New York, 1984; and Pennington et al., Peptide Synthesis Protocols, Humana Press, Totowa, N.J., 1994). Additionally, many companies offer custom peptide synthesis services.
The PBRC linked purification moieties described herein can also be produced by direct chemical synthesis. For example, the PBRC linked purification moieties described herein can be produced as modified polypeptides, with nonpeptide moieties attached by covalent linkage to the N-terminus and/or C-terminus. In certain embodiments, either the carboxy-terminus or the amino-terminus, or both, are chemically modified. Common modifications of the terminal amino and carboxyl groups, include, but are not limited to acetylation and amidation, respectively. Amino-terminal modifications such as acylation (e.g., acetylation) or alkylation (e.g., methylation) and carboxy-terminal-modifications such as amidation, as well as other terminal modifications, including cyclization, can be incorporated into various embodiments. Certain amino-terminal and/or carboxy-terminal modifications and/or polypeptide extensions to the core sequence can provide advantageous physical, chemical, biochemical, and pharmacological properties, such as: enhanced stability, increased potency and/or efficacy, resistance to serum proteases, desirable pharmacokinetic properties, and others.
The PBRC linked purification moieties can be prepared using recombinant DNA and molecular cloning techniques. Genes encoding the PBRC linked purification moieties may be produced in heterologous host cells, particularly in the cells of microbial hosts. Any techniques for transfecting host cells and purifying proteins and polypeptides known in the art can be used in connection with the methods described herein. Exemplary epitope tags suitable for use with the methods described herein include, but are not limited to FLAG, HA, Myc and T7 epitope tags. The PBRTs, PBRCs or PBRC linked purification moieties described herein can be synthesized chemically using standard polypeptide synthesis techniques.
The invention also extends to the DNA expression vector comprising DNA coding for the PBRTs or PBRCs described herein, whether or not the encoded products further comprise a linked purification moiety. The invention also provides the expression vector comprising sequences coding for a PBRT or a PBRC configured to allow insertion of a DNA sequence downstream of the sequence coding for the PBRT or the PBRC so as to facilitate production of a fusion protein comprising a PBRT or a PBRC. For example, such vectors can comprise one or more cloning sites between the sequence coding for the PBRT or the PBRC to enable generation of an in-frame translation product. Such vectors may comprise multiple cloning sites in any of three reading frames. Methods for generating such expression vectors are well known in the art.
A variety of expression systems can be used to produce the PBRCs and PBRC linked purification moieties described herein. Such expression systems include vector based expression systems. Exemplary vector base expression systems suitable for use with the methods described herein include, but are not limited to, chromosomal, episomal and virus-derived vectors, e.g., vectors derived from bacterial plasmids, from bacteriophage, from transposons, from insertion elements, from yeast episomes, from viruses such as baculoviruses, retroviruses and vectors derived from combinations thereof such as those derived from plasmid and bacteriophage genetic elements, such as cosmids and phagemids.
The expression system vectors may contain regulatory regions that regulate as well as engender expression. In general, any system or vector suitable to maintain, propagate or express polynucleotide or polypeptide in a host cell may be used for expression in this regard. Expression systems and expression vectors can contain regulatory sequences that direct high level expression of foreign proteins relative to the growth of the host cell. Regulatory sequences are well known to those skilled in the art and examples include, but are not limited to, those which cause the expression of a gene to be turned on or off in response to a chemical or physical stimulus, including the presence of regulatory elements in the vector, for example, enhancer sequences. Any of these could be used to construct chimeric genes for production of the any of the binding peptides of the present invention. These chimeric genes could then be introduced into appropriate microorganisms via transformation to provide high level expression of the peptides.
A number of recombinant expression vectors can be used for expression of the PBRCs and PBRC linked purification moieties described herein. For example, the PBRT linked purification moieties described herein can be expressed in bacterial cells such as E. coli, insect cells (e.g., using baculovirus expression vectors), yeast cells, amphibian cells, or mammalian cells. Suitable host cells are well known to one skilled in the art. Alternatively, the recombinant expression vector can be transcribed and translated in vitro, using, for example T7 promoter regulatory sequences and T7 polymerase.
Examples of E. coli expression vectors include pTrc (Amann E et al., Gene 69:301-15 (1988)) and pET 11d (Studier et al., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) pp. 60-89). Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp-lac fusion promoter. Target gene expression from the pET 11d vector relies on transcription from a T7 gn10-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7 gn1). This viral polymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from a resident prophage harboring a T7 gn1 gene under the transcriptional control of the lacUV 5 promoter.
One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman S, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) pp. 119-28). Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (Wada K et al., Nucleic Acids Res. 20(Suppl.):2111-18 (1992)). Such alteration of nucleic acid sequences can be carried out by standard DNA synthesis techniques.
In another approach, a nucleic acid can be expressed in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed B, Nature 329:840-41 (1987)) and pMT2PC (Kaufman R J et al., EMBO J. 6:187-95 (1987)). When used in mammalian cells, the expression vector's control functions can be provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalovirus, and Simian Virus 40. For other suitable expression systems for both prokaryotic and eukaryotic cells, see chapters 16 and 17 of Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.
A number of these methodologies can also be applied in vivo, systemically or locally, in a complex biological system such as a human. For example, increased copy number of nucleic acids PBRC or PBRC linked purification moieties described herein in expressible from (by DNA transfection), can be employed.
Nucleic acid purification moieties encoding PBRT or PBRC linked purification moieties described herein can be administered to cells by a variety of methods known to those of skill in the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as biodegradable polymers, hydrogels, cyclodextrins (see for example, Gonzalez et al., Bioconjugate Chem. 10:1068-1074, 1999; Wang et al., International PCT Publication Nos. WO 03/47518 and WO 03/46185), poly(lactic-co-glycolic)acid (PLGA) and PLCA microspheres (see for example, U.S. Pat. No. 6,447,796 and U.S. Patent Application Publication No. US 2002130430), biodegradable nanocapsules, and bioadhesive microspheres, or by proteinaceous vectors (O'Hare and Normand, International PCT Publication No. WO 00/53722).
This invention may also be of use in the pharmaceutical/biotechnology industry where therapeutic compounds need to be purified in large quantities. This approach provides very pure product in a very quick manner.
Purification moieties that can be linked to the PBRTs or PBRCs described herein can be any purification moiety, including a biologically active protein (e.g., a therapeutic peptide, protein or an enzyme useful in industrial biocatalysis).
The purification moieties suitable for use with the methods described herein can be of widely varying types, including, for example, peptides, non-peptide proteins, lipids, oligonucleotides and carbohydrates, or alternatively a ligand-binding protein or an active fragment thereof having binding affinity to a molecule selected from the group consisting of small organic or inorganic molecules, proteins, peptides, single-stranded or double-stranded oligonucleotides, polynucleotides, lipids, and carbohydrates.
Suitable purification moieties include, but are not limited to, molecules useful in medicine, agriculture and other scientific and industrial fields. For example, suitable molecules include those of interest in medicine, agriculture or other scientific or industrial fields. Examples of suitable proteins include enzymes utilized in replacement therapy; hormones for promoting growth in animals, or cell growth in cell culture; and active proteinaceous substances used in various applications, e.g., in biotechnology or in medical diagnostics. One of skill in the art will recognize that many types of recombinant polypeptides can be produced using the methods described herein. The present invention is not limited to any specific types of recombinant polypeptide described herein. Instead, it encompasses any and all recombinant polypeptides.
The PBRTs or PBRCs described herein can be joined to a purification moiety from any source or origin and can include a polypeptide found in prokaryotes, viruses, and eukaryotes, including fungi, plants, yeasts, insects, and animals, including mammals (e.g. humans). Purification moieties suitable for use with the methods described herein include, but are not limited to any polypeptide sequences, known or hypothetical or unknown, which can be identified using common sequence repositories. Examples of such sequence repositories, include, but are not limited to GenBank EMBL, DDBJ and the NCBI. Other repositories can easily be identified by searching on the internet. Polypeptides that can be produced using the methods described herein also include polypeptides have at least about 60%, 70%, 75%, 80%, 90%, 95%, or at least about 99% or more identity to any known or available polypeptide (e.g., a therapeutic polypeptide, a diagnostic polypeptide, an industrial enzyme, or portion thereof, and the like).
Purification moieties suitable for use with the methods described herein include, but are not limited to, polypeptides comprising one or more non-natural amino acids.
Purification moieties suitable for use with the methods described herein include, but are not limited to, cytokines, inflammatory molecules, growth factors, their receptors, and oncogene products or portions thereof. Examples of cytokines, inflammatory molecules, growth factors, their receptors, and oncogene products include, but are not limited to e.g., alpha-1 antitrypsin, Angiostatin, Antihemolytic factor, antibodies (including an antibody or a functional fragment or derivative thereof selected from: Fab, Fab′, F(ab)2, Fd, Fv, ScFv, diabody, tribody, tetrabody, dimer, trimer or minibody), angiogenic molecules, angiostatic molecules, Apolipopolypeptide, Apopolypeptide, Asparaginase, Adenosine deaminase, Atrial natriuretic factor, Atrial natriuretic polypeptide, Atrial peptides, Angiotensin family members, Bone Morphogenic Polypeptide (BMP-1, BMP-2, BMP-3, BMP-4, BMP-5, BMP-6, BMP-7, BMP-8a, BMP-8b, BMP-10, BMP-15, etc.); C—X—C chemokines (e.g., T39765, NAP-2, ENA-78, Gro-a, Gro-b, Gro-c, IP-10, GCP-2, NAP-4, SDF-1, PF4, MIG), Calcitonin, CC chemokines (e.g., Monocyte chemoattractant polypeptide-1, Monocyte chemoattractant polypeptide-2, Monocyte chemoattractant polypeptide-3, Monocyte inflammatory polypeptide-1 alpha, Monocyte inflammatory polypeptide-1 beta, RANTES, 1309, R83915, R91733, HCC1, T58847, D31065, T64262), CD40 ligand, C-kit Ligand, Ciliary Neurotrophic Factor, Collagen, Colony stimulating factor (CSF), Complement factor 5a, Complement inhibitor, Complement receptor 1, cytokines, (e.g., epithelial Neutrophil Activating Peptide-78, GRO alpha/MGSA, GRO beta, GRO gamma, MIP-1 alpha, MIP-1 delta, MCP-1), deoxyribonucleic acids, Epidermal Growth Factor (EGF), Erythropoietin (“EPO”, representing a preferred target for modification by the incorporation of one or more non-natural amino acid), Exfoliating toxins A and B, Factor IX, Factor VII, Factor VIII, Factor X, Fibroblast Growth Factor (FGF), Fibrinogen, Fibronectin, G-CSF, GM-CSF, Glucocerebrosidase, Gonadotropin, growth factors, Hedgehog polypeptides (e.g., Sonic, Indian, Desert), Hemoglobin, Hepatocyte Growth Factor (HGF), Hepatitis viruses, Hirudin, Human serum albumin, Hyalurin-CD44, Insulin, Insulin-like Growth Factor (IGF-I, IGF-II), interferons (e.g., interferon-alpha, interferon-beta, interferon-gamma, interferon-epsilon, interferon-zeta, interferon-eta, interferon-kappa, interferon-lambda, interferon-T, interferon-zeta, interferon-omega), glucagon-like peptide (GLP-1), GLP-2, GLP receptors, glucagon, other agonists of the GLP-1R, natriuretic peptides (ANP, BNP, and CNP), Fuzeon and other inhibitors of HIV fusion, Hurudin and related anticoagulant peptides, Prokineticins and related agonists including analogs of black mamba snake venom, TRAIL, RANK ligand and its antagonists, calcitonin, amylin and other glucoregulatory peptide hormones, and Fc fragments, exendins (including exendin-4), exendin receptors, interleukins (e.g., IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, etc.), I-CAM-1/LFA-1, Keratinocyte Growth Factor (KGF), Lactoferrin, leukemia inhibitory factor, Luciferase, Neurturin, Neutrophil inhibitory factor (NIF), oncostatin M, Osteogenic polypeptide, Parathyroid hormone, PD-ECSF, PDGF, peptide hormones (e.g., Human Growth Hormone), Oncogene products (Mos, Rel, Ras, Raf, Met, etc.), Pleiotropin, Polypeptide A, Polypeptide G, Pyrogenic exotoxins A, B, and C, Relaxin, Renin, ribonucleic acids, SCF/c-kit, Signal transcriptional activators and suppressors (p53, Tat, Fos, Myc, Jun, Myb, etc.), Soluble complement receptor 1, Soluble I-CAM 1, Soluble interleukin receptors (IL-1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15), soluble adhesion molecules, Soluble TNF receptor, Somatomedin, Somatostatin, Somatotropin, Streptokinase, Superantigens, i.e., Staphylococcal enterotoxins (SEA, SEB, SEC1, SEC2, SEC3, SED, SEE), Steroid hormone receptors (such as those for estrogen, progesterone, testosterone, aldosterone, LDL receptor ligand and corticosterone), Superoxide dismutase (SOD), Toll-like receptors (such as Flagellin), Toxic shock syndrome toxin (TSST-1), Thymosin a 1, Tissue plasminogen activator, transforming growth factor (TGF-alpha, TGF-beta), Tumor necrosis factor beta (TNF beta), Tumor necrosis factor receptor (TNFR), Tumor necrosis factor-alpha (TNF alpha), transcriptional modulators (for example, genes and transcriptional modular polypeptides that regulate cell growth, differentiation and/or cell regulation), Vascular Endothelial Growth Factor (VEGF), virus-like particle, VLA-4/VCAM-1, Urokinase, signal transduction molecules, estrogen, progesterone, testosterone, aldosterone, LDL, corticosterone.
Additional purification moieties suitable for use with the methods described herein include, but are not limited to, enzymes (e.g., industrial enzymes) or portions thereof. Examples of enzymes include, but are not limited to amidases, amino acid racemases, acylases, dehalogenases, dioxygenases, diarylpropane peroxidases, epimerases, epoxide hydrolases, esterases, isomerases, kinases, glucose isomerases, glycosidases, glycosyl transferases, haloperoxidases, monooxygenases (e.g., p450s), lipases, lignin peroxidases, nitrile hydratases, nitrilases, proteases, phosphatases, subtilisins, transaminase, and nucleases. In certain embodiments, such enzymes comprising a PBRT or PBRC can be used as immobilized enzymes in industrial biocatalysis. The enzymes comprising a PBRTs or a PBRC can also be added to a solution to facilitate biocatalysis and then reisolated from the solution.
Additional purification moieties suitable for use with the methods described herein include, but are not limited to, agriculturally related polypeptides such as insect resistance polypeptides (e.g., Cry polypeptides), starch and lipid production enzymes, plant and insect toxins, toxin-resistance polypeptides, Mycotoxin detoxification polypeptides, plant growth enzymes (e.g., Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase), lipoxygenase, and Phosphoenolpyruvate carboxylase.
Additional purification moieties suitable for use with the methods described herein include, but are not limited to, antibodies, immunoglobulin domains of antibodies and their fragments. Examples of antibodies include, but are not limited to antibodies, antibody fragments, antibody derivatives, Fab fragments, Fab′ fragments, F(ab)2 fragments, Fd fragments, Fv fragments, single-chain Fv fragments (scFv), diabodies, tribodies, tetrabodies, dimers, trimers, and minibodies.
Additional purification moieties suitable for use with the methods described herein include, but are not limited to, prophylactic vaccine or therapeutic vaccine polypeptides. A prophylactic vaccine is one administered to subjects who are not infected with a condition against which the vaccine is designed to protect. In certain embodiments, a preventive vaccine will prevent a virus from establishing an infection in a vaccinated subject. However, even if it does not provide complete protective immunity, a prophylactic vaccine may still confer some protection to a subject. For example, a prophylactic vaccine may decrease the symptoms, severity, and/or duration of the disease. A therapeutic vaccine, is administered to reduce the impact of a viral infection in subjects already infected with that virus. A therapeutic vaccine may decrease the symptoms, severity, and/or duration of the disease. Vaccine polypeptides include polypeptides, or polypeptide fragments from infectious fungi (e.g., Aspergillus, Candida species) bacteria (e.g. E. coli, Staphylococci aureus)), or Streptococci (e.g., pneumoniae); protozoa such as sporozoa (e.g., Plasmodia), rhizopods (e.g., Entamoeba) and flagellates (Trypanosoma, Leishmania, Trichomonas, Giardia, etc.); viruses such as (+) RNA viruses (examples include Poxviruses e.g., vaccinia; Picornaviruses, e.g., polio; Togaviruses, e.g., rubella; Flaviviruses, e.g., HCV; and Coronaviruses), (−) RNA viruses (e.g., Rhabdoviruses, e.g., VSV; Paramyxovimses, e.g., RSV; Orthomyxovimses, e.g., influenza; Bunyaviruses; and Arenaviruses), dsDNA viruses (Reoviruses, for example), RNA to DNA viruses, i.e., Retroviruses, e.g., HIV and HTLV, and certain DNA to RNA viruses such as Hepatitis B.
Additional purification moieties suitable for use with the methods described herein include, but are not limited to, molecules that comprise a chemical moiety selected from the group consisting of: cytotoxins, pharmaceutical drugs, dyes or fluorescent labels, a nucleophilic or electrophilic group, a ketone or aldehyde, azide or alkyne compounds, photocaged groups, tags, a peptide, a polypeptide, a polypeptide, an oligosaccharide, polyethylene glycol with any molecular weight and in any geometry, polyvinyl alcohol, metals, metal complexes, polyamines, imidizoles, carbohydrates, lipids, biopolymers, particles, solid supports, a polymer, a targeting agent, an affinity group, any agent to which a complementary reactive chemical group can be attached, biophysical or biochemical probes, isotypically-labeled probes, spin-label amino acids, fluorophores, aryl iodides and bromides.
Reference is also made to a “variant PBRT.” A variant PBRT is a PBRT comprising one or more amino acid substitutions any position in the sequence of SEQ ID NO: 1 wherein the substitution replaces any amino acid in position 1 through 9 with an amino acid having a similar side chain group, an amino acid having a similar side chain configuration, an amino acid having an evolutionary positive relatedness, or an amino acid having an evolutionary neutral relatedness.
As used herein, the term “variant precipitable-beta roll cassette” (PBRC) refers to an amino acid sequence comprising at least one variant PBRT. In certain embodiments, a variant PBRC will comprise at least two variant PBRTs. In certain embodiments, a variant PBRC will comprise at least 3 variant PBRTs, at least 4 variant PBRTs, at least 5 variant PBRTs, at least 6 variant PBRTs, at least 7 variant PBRTs, at least 8 variant PBRTs, at least 9 variant PBRTs, at least 10 variant PBRTs, at least 11 variant PBRTs, at least 12 variant PBRTs, at least 13 variant PBRTs, at least 14 variant PBRTs, at least 15 variant PBRTs, at least 16 variant PBRTs, at least 17 variant PBRTs, at least 18 variant PBRTs, at least 19 variant PBRTs, at least 20 variant PBRTs, or 20 or more variant PBRTs. In certain embodiments, the PBRCs described herein will comprise a plurality of variant precipitable beta roll tags arranged in a tandem repeat. For example, in certain embodiments, the variant PBRCs described herein can comprise at least 2 variant PBRTs, at least 3 variant PBRTs, at least 4 variant PBRTs, at least 5 variant PBRTs, at least 6 variant PBRTs, at least 7 variant PBRTs, at least 8 variant PBRTs, at least 9 variant PBRTs, at least 10 variant PBRTs, at least 11 variant PBRTs, at least 12 variant PBRTs, at least 13 variant PBRTs, at least 14 variant PBRTs, at least 15 variant PBRTs, at least 16 variant PBRTs, at least 17 variant PBRTs, at least 18 variant PBRTs, at least 19 variant PBRTs, at least 20 variant PBRTs, or 20 or more variant PBRTs in tandem repeat. In certain embodiments, a PBRC can comprise at least two PBRCs separated by a linking amino acid sequence. Where a linking amino acid sequence in present between two PBRTs, a PBRTs located at either end of the linking sequence can be an individual PBRT or it can be a PBRTs that is part of a tandem arrangement.
Thus in certain embodiments, a variant PBRC will comprise at least 2 variant PBRCs, at least variant 3 PBRTs, at least 4 variant PBRTs, at least 5 variant PBRTs, at least 6 variant PBRTs, at least 7 variant PBRTs, at least 8 variant PBRTs, at least 9 variant PBRTs, at least 10 variant PBRTs, at least 11 variant PBRTs, at least 12 variant PBRTs, at least 13 variant PBRTs, at least 14 variant PBRTs, at least 15 variant PBRTs, at least 16 variant PBRTs, at least 17 variant PBRTs, at least 18 variant PBRTs, at least 19 variant PBRTs, at least 20 variant PBRTs, or 20 or more variant PBRTs, all of which are located N-terminally to a CS. In certain embodiments, a variant PBRC will comprise at least 2 variant PBRCs, at least variant 3 PBRTs, at least 4 variant PBRTs, at least 5 variant PBRTs, at least 6 variant PBRTs, at least 7 variant PBRTs, at least 8 variant PBRTs, at least 9 variant PBRTs, at least 10 variant PBRTs, at least 11 variant PBRTs, at least 12 variant PBRTs, at least 13 variant PBRTs, at least 14 variant PBRTs, at least 15 variant PBRTs, at least 16 variant PBRTs, at least 17 variant PBRTs, at least 18 variant PBRTs, at least 19 variant PBRTs, at least 20 variant PBRTs, or 20 or more variant PBRTs, all of which are located C-terminally to a CS.
In certain aspects, the invention relates to a variant PBRT that contains one or more amino acid insertions, deletions or substitutions as compared to the sequence of SEQ ID NO: 1 and wherein the variant PBRT retains an ability to bind to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the PBRT.
Changes can be introduced by mutation into nucleic acid sequences, thereby leading to changes in the amino acid sequence of the encoded protein, without altering the functional activity of a PBRT or a PBRC. For example, nucleotide substitutions leading to amino acid substitutions at non-essential amino acid residues can be made in the sequence of a PBRT or a PBRC. A non-essential amino acid residue is a residue that can be altered from the sequence of an amino acid of this invention without altering the ability of the PBRT or PBRC to bind to bind to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the PBRT or PBRC.
Exemplary residues which are non-essential and therefore amenable to substitution to generate the variant PBRTs and PBRCs described herein can be identified by one of ordinary skill in the art by performing an amino acid alignment of two more PBRTs or PBRCs and determining residues that are not required for the PBRT or PBRC to bind to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the PBRT or PBRC.
Mutations can be introduced randomly along all or part of a nucleic acid sequence encoding a PBRT or PBRC, such as by saturation mutagenesis, and the resultant mutants can be screened, for example, for their ability bind to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT or variant PBRC. Following mutagenesis, the purification moiety linked to the variant PBRT or variant PBRC can be expressed recombinantly in a host cell and the functional activity of the precipitable beta-roll tag can be determined using assays available in the art for assessing binding to Ca2+, undergoing reversible precipitation in the presence of Ca2+, or inducing reversible precipitation of purification moiety linked to the variant PBRT or variant PBRC. In certain embodiments, the variant PBRTs described herein can comprise one or more amino acid substitutions, insertions or deletions, wherein the variant PBRT is functionally equivalent a PBRT having the sequence GGAGNDTLY (SEQ ID No. 1). In one embodiment, the variant PBRT has an identical ability bind to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety in a manner similar to, but not necessarily identical to a PBRC comprising only PBRTs of the sequence GGAGNDTLY (SEQ ID NO: 1). In one embodiment, the variant PBRT has a reduced ability bind to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety in a manner similar to, but not necessarily identical to a PBRC comprising only PBRTs of the sequence GGAGNDTLY (SEQ ID NO: 1). In one embodiment, the variant PBRT has an increased ability bind to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety in a manner similar to, but not necessarily identical to a PBRC comprising only PBRTs of the sequence GGAGNDTLY (SEQ ID NO: 1).
The variant PBRCs described herein can also comprise on or more PBRTs in addition to one or more variant PBRTs. The variant PBRCs described herein can also be employed in any embodiments or configuration described herein for a PBRC. Thus, the description of a composition comprising a PBRC, or a method comprising a PBRC applies equally to a variant PBRT or a variant PBRC so long as the variant PBRT or the variant PBRC can bind to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety in a manner similar to, but not necessarily identical to a PBRC comprising only PBRTs of the sequence GGAGNDTLY (SEQ ID NO: 1).
In one embodiment, a variant PBRT comprises the sequence GGXGXDXXX (SEQ ID NO: 2) wherein X can be selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine. In one embodiment, the variant PBRT has a sequence of GGXGXDXXX (SEQ ID NO: 2), wherein X is not proline. In one embodiment, the variant PBRT comprises the sequence GGXGXDXXX (SEQ ID NO: 2) wherein X is a natural or non-natural amino acid comprising a modification.
In one embodiment, a variant PBRT or PBRC comprises an amino acid sequence having at least about 75%, 80%, 85%, 90%, 95%, 98%, 99% identity with an amino acid sequence of SEQ ID NO: 1.
As used herein, “sequence identity” means the percentage of identical nucleotide or amino acid residues at corresponding positions in two or more sequences when the sequences are aligned to maximize sequence matching, i.e., taking into account gaps and insertions. The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. Techniques for determining sequence identity are well known to one skilled in the art, and include, for example, analysis with a sequence comparison algorithm or FASTA version 3.0t78 using default parameters (Pearson and Lipman, Proc Natl Acad Sci USA. 1988 April; 85(8):2444-8). In another non-limiting example, scoring of amino acid can be calculated using the PAM250 matrix as described in Dayhoff et al., (1978) in Atlas of Protein Sequence and Structure, ed. Dayhoff, M. (Natl. Biomed. Res. Found., Silver Spring, Md.), Vol. 5, Suppl. 3, pp. 345-352.
Percent identity or percent similarity of a DNA or peptide sequence can be determined, for example, by comparing sequence information using the GAP computer program. The GAP program utilizes the alignment method of Needleman et al., 1970, as revised by Smith et al., 1981. Briefly, the GAP program defines similarity as the number of aligned symbols (i.e., nucleotides or amino acids) that are similar, divided by the total number of symbols in the shorter of the two sequences. The preferred parameters for the GAP program are the default parameters, which do not impose a penalty for end gaps. See e.g., Schwartz et al., 1979; Gribskov et al., 1986. Nucleic acids that differ due to degeneracy of the genetic code, and still encode the PBRTs or PBRCs, described herein are encompassed by the present disclosure.
Variants can be produced by any number of methods, including but not limited to, error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site-specific mutagenesis, gene reassembly, and any combination thereof.
Variant PBRTs or variant PBRCs falling within the scope of this invention, can, in general, be generated by selecting substitutions that do not differ significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, (b) the charge or hydrophobicity of the purification moiety at the target site, or (c) the bulk of the side chain.
In one embodiment, a variant PBRT or a variant PBRC can comprise a conservative amino acid substitution in which an amino acid residue is replaced with an amino acid residue having a similar side chain configuration. Amino acid residues having similar side chain configurations have been defined in the art within in accordance with the following categories: basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine), aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine), aliphatic side chains (e.g., glycine, alanine, valine, leucine, isoleucine), and sulfur-containing side chains (methionine, cysteine). Substitutions can also be made between acidic amino acids and their respective amides (e.g., asparagine and aspartic acid, or glutamine and glutamic acid).
In one embodiment, a variant PBRT or a variant PBRC can comprise a conservative amino acid substitution in which an amino acid residue is replaced with an amino acid residue having a similar side chain group Amino acid residues having similar side chain groups have been defined in the art within in accordance with the following categories: a no side chain group (glycine), an aliphatic side chain group (alanine, valine, leucine, isoleucine, proline), a hydroxyl side chain group (serine, threonine), an acidic side chain group (aspartic acid, glutamic acid), an amide side chain group (asparagine, glutamine), a basic side chain group (lysine, arginine), an imidazole side chain group (histidine), an aromatic side chain group (phenylalanine, tyrosine, tryptophan), and a sulfur containing side chain group (methionine, cysteine) (see Sambrook et al, (2001) Molecular Cloning: A Laboratory Manual, Volume 3, Table A7-4).
In one embodiment, a variant PBRT or a variant PBRC can comprise a conservative amino acid substitution in which an amino acid residue is replaced an amino acid having evolutionarily positive relatedness. Amino acids having evolutionarily positive relatedness have been defined in the art as follows (wherein the amino acid(s) having evolutionarily positive relatedness are indicated in parentheses): Alanine (serine, threonine, proline, glycine); Arginine (glutamine, histidine, lysine, tryptophan); Asparagine (serine, threonine, aspartic acid, glutamic acid, glutamine, histidine, lysine); Aspartic acid (threonine, glycine, asparagine, glutamine, glutamic acid, histidine); Glutamic acid (threonine, asparagine, aspartic acid, glutamine, histidine); Glutamine (asparagine, aspartic acid, glutamic acid, histidine, arginine, lysine); Glycine (serine, threonine, alanine, aspartic acid); Histidine (asparagine, aspartic acid, glutamine, arginine); Isoleucine (threonine, methionine, leucine, valine, phenylalanine); Leucine (methionine, isoleucine, valine, phenylalanine); Lysine (threonine, asparagine, glutamine, arginine); Methionine (isoleucine, leucine, valine); Phenylalanine (isoleucine, leucine, tyrosine); Proline (serine, threonine, alanine); Serine (threonine, proline, alanine, glycine, asparagine); Threonine (serine, proline, alanine, glycine, asparagine, aspartic acid, glutamic acid, lysine, isoleucine, valine); Tryptophan (arginine, tyrosine); Tyrosine (phenylalanine, tryptophan); Valine (threonine, methionine, isoleucine, leucine) (see Dayhoff et al., (1978) in Atlas of Protein Sequence and Structure, ed. Dayhoff, M., Natl. Biomed. Res. Found., Silver Spring, Md.), Vol. 5, Suppl. 3, pp. 345-352).
In one embodiment, variant of a variant PBRT or a variant PBRC can comprise a conservative amino acid substitution in which an amino acid residue is replaced an amino acid having evolutionarily positive relatedness. Amino acids having evolutionarily neutral relatedness have been defined in the art as follows (wherein the amino acid(s) having evolutionarily neutral relatedness are indicated in parentheses): Alanine (asparagine, aspartic acid, glutamine, glutamic acid, valine); Arginine (serine, proline, asparagine, methionine); Asparagine (alanine, glycine, arginine); Aspartic acid (serine, alanine, lysine); Cysteine (serine, tyrosine); Glutamic acid (serine, alanine, glycine, lysine); Glutamine (proline, alanine); Glycine (asparagine, glutamic acid); Histidine (proline, lysine, tyrosine); Lysine (serine, asparagine, glutamic acid, histidine, methionine); Methionine (arginine, lysine, phenylalanine); Phenylalanine (methionine, tryptophan); Proline (glutamine, histidine, arginine); Serine (cysteine, aspartic acid, glutamic acid, arginine, lysine); Threonine (none); Tryptophan (phenylalanine); Tyrosine (cysteine, histidine); Valine (alanine) (see Dayhoff et al., (1978) in Atlas of Protein Sequence and Structure, ed. Dayhoff, M., Natl. Biomed. Res. Found, Silver Spring, Md.), Vol. 5, Suppl. 3, pp. 345-352).
In one embodiment of a variant PBRT, the glycine at position 1 of SEQ ID NO: 1 is not mutated.
In another embodiment of a variant PBRT, the glycine at position 1 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the glycine is replaced with an amino acid having an uncharged polar side chain configuration (e.g., asparagine, glutamine, serine, threonine, tyrosine, or cysteine).
In another embodiment of a variant PBRT, the glycine at position 1 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the glycine is replaced with an amino acid having an aliphatic side chain configuration (e.g., alanine, valine, leucine, isoleucine)
In another embodiment of a variant PBRT, the glycine at position 1 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily positive relatedness such that the glycine is replaced with any of serine, threonine, alanine, or aspartic acid.
In another embodiment of a variant PBRT, the glycine at position 1 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily neutral relatedness such that the glycine is replaced with any of asparagine or glutamic acid.
In one embodiment of a variant PBRT, mutation of the glycine at position 1 of SEQ ID NO: 1 to any of alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine wherein mutation of the glycine at position 1 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, mutation of the glycine at position 1 of SEQ ID NO: 1 is with a non-natural or synthetic amino acid wherein mutation of the glycine at position 1 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, the glycine at position 2 of SEQ ID NO: 1 can be mutated to an asparagine residue.
In one embodiment of a variant PBRT, the glycine at position 2 of SEQ ID NO: 1 can be mutated to an aspartic acid residue.
In another embodiment of a variant PBRT, the glycine at position 2 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the glycine is replaced with an amino acid having an uncharged polar side chain configuration (e.g., asparagine, glutamine, serine, threonine, tyrosine, or cysteine).
In another embodiment of a variant PBRT, the glycine at position 2 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the glycine is replaced with an amino acid having an aliphatic side chain configuration (e.g., alanine, valine, leucine, isoleucine)
In another embodiment of a variant PBRT, the glycine at position 2 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily positive relatedness such that the glycine is replaced with any of serine, threonine, alanine, or aspartic acid.
In another embodiment of a variant PBRT, the glycine at position 2 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily neutral relatedness such that the glycine is replaced with any of asparagine or glutamic acid.
In one embodiment of a variant PBRT, mutation of the glycine at position 2 of SEQ ID NO: 1 to any of alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine wherein mutation of the glycine at position 2 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, mutation of the glycine at position 2 of SEQ ID NO: 1 is with a non-natural or synthetic amino acid wherein mutation of the glycine at position 2 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, the alanine at position 3 of SEQ ID NO: 1 can be mutated to a serine, glycine, or aspartic acid residue.
In one embodiment of a variant PBRT, the alanine at position 3 of SEQ ID NO: 1 can be mutated to a glutamic acid, leucine, or asparagine residue.
In one embodiment of a variant PBRT, the alanine at position 3 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the alanine is replaced with an amino acid having a nonpolar side chain configuration (e.g., valine, leucine, isoleucine, proline, phenylalanine, methionine, or tryptophan).
In one embodiment of a variant PBRT, the alanine at position 3 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the alanine is replaced with an amino acid having an aliphatic side chain configuration (e.g., glycine, valine, leucine, isoleucine)
In another embodiment of a variant PBRT, the alanine at position 3 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain group such that the alanine is replaced with an amino acid having an aliphatic side chain group (e.g., valine, leucine, isoleucine, proline).
In another embodiment of a variant PBRT, the alanine at position 3 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily positive relatedness such that the alanine is replaced with any of serine, threonine, proline, or glycine.
In another embodiment of a variant of a precipitable beta-roll tag, the at position 3 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily neutral relatedness such that the alanine is replaced with any of asparagine, aspartic acid, glutamine, glutamic acid, or valine.
In one embodiment of a variant PBRT, mutation of the alanine at position 3 of SEQ ID NO: 1 to any of glycine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine wherein mutation of the alanine at position 3 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, mutation of the alanine at position 3 of SEQ ID NO: 1 is with a non-natural or synthetic amino acid wherein mutation of the alanine at position 3 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, the glycine at position 4 of SEQ ID NO: 1 can be mutated to an alanine residue.
In another embodiment of a variant PBRT, the glycine at position 4 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the glycine is replaced with an amino acid having an uncharged polar side chain configuration (e.g., asparagine, glutamine, serine, threonine, tyrosine, or cysteine).
In another embodiment of a variant PBRT, the glycine at position 4 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the glycine is replaced with an amino acid having an aliphatic side chain configuration (e.g., alanine, valine, leucine, isoleucine)
In another embodiment of a variant PBRT, the glycine at position 4 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily positive relatedness such that the glycine is replaced with any of serine, threonine, alanine, or aspartic acid.
In another embodiment of a variant PBRT, the glycine at position 4 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily neutral relatedness such that the glycine is replaced with any of asparagine or glutamic acid.
In one embodiment of a variant PBRT, mutation of the glycine at position 4 of SEQ ID NO: 1 to any of alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine wherein mutation of the glycine at position 4 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, mutation of the glycine at position 4 of SEQ ID NO: 1 is with a non-natural or synthetic amino acid wherein mutation of the glycine at position 4 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, the asparagine at position 5 of SEQ ID NO: 1 can be mutated to an aspartic acid or alanine residue.
In one embodiment of a variant PBRT, the asparagine at position 5 of SEQ ID NO: 1 can be mutated to a serine residue.
In one embodiment of a variant PBRT, the asparagine at position 5 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the asparagine is replaced with an amino acid having an uncharged polar side chain configuration (e.g., glycine, glutamine, serine, threonine, tyrosine, cysteine)
In one embodiment of a variant PBRT, the asparagine at position 5 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the asparagine is replaced with an amino acid having a the side chain configuration of its amide (e.g., aspartic acid).
In another embodiment of a variant PBRT, the asparagine at position 5 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain group such that the asparagine is replaced with an amino acid having an amide side chain group (e.g., glutamine).
In another embodiment of a variant PBRT, the asparagine at position 5 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily positive relatedness such that the asparagine is replaced with any of serine, threonine, aspartic acid, glutamic acid, glutamine, histidine, or lysine.
In another embodiment of a variant PBRT, the asparagine at position 5 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily neutral relatedness such that the asparagine is replaced with any of alanine, glycine, or arginine.
In one embodiment of a variant PBRT, mutation of the asparagine at position 5 of SEQ ID NO: 1 to any of glycine, alanine, arginine, aspartic acid, cysteine, glutamic acid, glutamine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine wherein mutation of the asparagine at position 5 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, mutation of the asparagine at position 5 of SEQ ID NO: 1 is with a non-natural or synthetic amino acid wherein mutation of the asparagine at position 5 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, the aspartic acid at position 6 of SEQ ID NO: 1 can be mutated to an asparagine residue.
In one embodiment of a variant PBRT, the aspartic acid at position 6 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the aspartic acid is replaced with an amino acid having an acidic side chain configuration (e.g., glutamic acid).
In one embodiment of a variant PBRT, the aspartic acid at position 6 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the aspartic acid is replaced with an amino acid having a the side chain configuration of its amide (e.g., asparagine).
In another embodiment of a variant PBRT, the aspartic acid at position 6 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain group such that the aspartic acid is replaced with an amino acid having an acidic side chain group (e.g., glutamic acid).
In another embodiment of a variant PBRT, the aspartic acid at position 6 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily positive relatedness such that the aspartic acid is replaced with any of threonine, glycine, asparagine, glutamine, glutamic acid, or histidine.
In another embodiment of a variant PBRT, the aspartic acid at position 6 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily neutral relatedness such that the aspartic acid is replaced with any of serine, alanine, or lysine.
In one embodiment of a variant PBRT, mutation of the aspartic acid at position 6 of SEQ ID NO: 1 to any of glycine, alanine, arginine, asparagine, cysteine, glutamic acid, glutamine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine wherein mutation of the aspartic acid at position 6 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, mutation of the aspartic acid at position 6 of SEQ ID NO: 1 is with a non-natural or synthetic amino acid wherein mutation of the aspartic acid at position 6 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, the threonine at position 7 of SEQ ID NO: 1 can be mutated to an isoleucine or valine residue.
In one embodiment of a variant PBRT, the threonine at position 7 of SEQ ID NO: 1 can be mutated to a leucine residue.
In one embodiment of a variant PBRT, the threonine at position 7 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the threonine is replaced with an amino acid having an uncharged polar side chain configuration (e.g., glycine, asparagine, glutamine, serine, tyrosine, or cysteine).
In one embodiment of a variant PBRT, the threonine at position 7 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the threonine is replaced with an amino acid having a beta-branched side chain configuration (e.g., valine, isoleucine).
In another embodiment of a variant PBRT, the threonine at position 7 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain group such that the threonine is replaced with an amino acid having an hydroxyl side chain group (e.g., serine).
In another embodiment of a variant PBRT, the threonine at position 7 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily positive relatedness such that the threonine is replaced with any of serine, proline, alanine, glycine, asparagine, aspartic acid, glutamic acid, lysine, isoleucine, or valine.
In one embodiment of a variant PBRT, mutation of the threonine at position 7 of SEQ ID NO: 1 to any of glycine, alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, tryptophan, tyrosine, valine wherein mutation of the threonine at position 7 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, mutation of the threonine at position 7 of SEQ ID NO: 1 is with a non-natural or synthetic amino acid wherein mutation of the threonine at position 7 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, the leucine at position 8 of SEQ ID NO: 1 can be mutated to an isoleucine residue.
In one embodiment of a variant PBRT, the leucine at position 8 of SEQ ID NO: 1 can be mutated to a phenylalanine residue.
In one embodiment of a variant PBRT, the leucine at position 8 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the leucine is replaced with an amino acid having a nonpolar side chain configuration (e.g., alanine, valine, isoleucine, proline, phenylalanine, methionine, or tryptophan).
In one embodiment of a variant PBRT, the leucine at position 8 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the leucine is replaced with an amino acid having an aliphatic side chain configuration (e.g., glycine, alanine, valine, or isoleucine).
In another embodiment of a variant PBRT, leucine at position 8 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain group such that the leucine is replaced with an amino acid having an aliphatic side chain group (e.g., alanine, valine, isoleucine, proline).
In another embodiment of a variant PBRT, the leucine at position 8 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily positive relatedness such that the leucine is replaced with any of methionine, isoleucine, valine, or phenylalanine.
In another embodiment of a variant PBRT, the leucine at position 8 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily neutral relatedness such that the leucine is replaced with any of serine, asparagine, glutamic acid, histidine, or methionine.
In one embodiment of a variant PBRT, mutation of the leucine at position 8 of SEQ ID NO: 1 to any of glycine, alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, histidine, isoleucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine wherein mutation of the leucine at position 8 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, mutation of the leucine at position 8 of SEQ ID NO: 1 non-natural amino acid wherein mutation of leucine at position 8 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, the tyrosine at position 9 of SEQ ID NO: 1 can be mutated to an isoleucine or valine residue.
In one embodiment of a variant PBRT, the tyrosine at position 9 of SEQ ID NO: 1 can be mutated to a phenylalanine, threonine, asparagine, aspartic acid, lysine, or serine residue.
In one embodiment of a variant PBRT, the tyrosine at position 9 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the tyrosine is replaced with an amino acid having an uncharged polar side chain configuration (e.g., glycine, asparagine, glutamine, serine, threonine, or cysteine).
In one embodiment of a variant PBRT, the tyrosine at position 9 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain configuration such that the tyrosine is replaced with an amino acid having an aromatic side chain configuration (e.g., tyrosine, phenylalanine, tryptophan, or histidine).
In another embodiment of a variant PBRT, the tyrosine at position 9 of SEQ ID NO: 1 can be mutated to an amino acid having a similar side chain group such that the tyrosine is replaced with an amino acid having an aromatic side chain group (e.g., phenylalanine, tryptophan).
In another embodiment of a variant PBRT, the tyrosine at position 9 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily positive relatedness such that the tyrosine is replaced with any of phenylalanine or tryptophan.
In another embodiment of a variant PBRT, the tyrosine at position 9 of SEQ ID NO: 1 can be mutated to an amino acid having evolutionarily neutral relatedness such that the tyrosine is replaced with any of cysteine or histidine.
In one embodiment of a variant PBRT, mutation of the tyrosine at position 9 of SEQ ID NO: 1 to any of glycine, alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine wherein mutation of tyrosine at position 9 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
In one embodiment of a variant PBRT, mutation of the tyrosine at position 9 of SEQ ID NO: 1 is with a non-natural or synthetic amino acid wherein mutation of the tyrosine at position 9 of SEQ ID NO: 1 will result in a precipitable beta-roll tag that is capable of binding to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the variant PBRT.
As described herein, a variant PBRC can further comprise a capping sequence. In certain embodiments, the capping sequence in a variant PBRC can be a variant capping sequence. A variant capping sequence can be an amino acid sequence having at least 70%, at least 80%, at least 90%, at least 95% or at least 98% identity to SEQ ID NO: 3. In another embodiment, a variant capping sequence is an amino acid sequence having at least 70%, at least 80%, at least 90%, at least 95% or at least 98% identity to any of SEQ ID NO: 4-23.
In still a further embodiment, a variant capping sequence is a sequence comprising one or more amino acid substitutions with an amino acid having a similar side chain group. In one embodiment, the variant capping sequence comprises the sequence of SEQ ID NO: 3 or any of SEQ ID NO: 4-23, wherein at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46, at least 47, at least 48, at least 49, at least 50, at least 51, at least 52, at least 53, at least 54, at least 55, at least 56, at least 57, at least 58, at least 59, at least 60, at least 61, at least 62, at least 63, at least 64, at least 65, at least 66, at least 67, or at least 68, amino acids in the sequence of SEQ ID NO: 3 or any of SEQ ID NO: 4-23 are substituted an amino acid having a similar side chain group.
In still a further embodiment, a variant capping sequence is a sequence comprising one or more amino acid substitutions with an amino acid having a similar side chain configuration. In one embodiment, the variant capping sequence comprises the sequence of SEQ ID NO: 3 or any of SEQ ID NO: 6-23, wherein at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46, at least 47, at least 48, at least 49, at least 50, at least 51, at least 52, at least 53, at least 54, at least 55, at least 56, at least 57, at least 58, at least 59, at least 60, at least 61, at least 62, at least 63, at least 64, at least 65, at least 66, at least 67, or at least 68, amino acids in the sequence of SEQ ID NO: 3 or any of SEQ ID NO: 6-23 are substituted an amino acid having a similar side chain configuration.
In still a further embodiment, a variant capping sequence is a sequence comprising one or more amino acid substitutions with an amino acid having evolutionarily positive relatedness. In one embodiment, the variant capping sequence comprises the sequence of SEQ ID NO: 3 or any of SEQ ID NO: 6-23, wherein at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46, at least 47, at least 48, at least 49, at least 50, at least 51, at least 52, at least 53, at least 54, at least 55, at least 56, at least 57, at least 58, at least 59, at least 60, at least 61, at least 62, at least 63, at least 64, at least 65, at least 66, at least 67, or at least 68, amino acids in the sequence of SEQ ID NO: 3 or any of SEQ ID NO: 6-23 are substituted an amino acid having evolutionarily positive relatedness.
In still a further embodiment, a variant capping sequence is a sequence comprising one or more amino acid substitutions with an amino acid having evolutionarily neutral relatedness. In one embodiment, the variant capping sequence comprises the sequence of SEQ ID NO: 3 or any of SEQ ID NO: 6-23, wherein at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46, at least 47, at least 48, at least 49, at least 50, at least 51, at least 52, at least 53, at least 54, at least 55, at least 56, at least 57, at least 58, at least 59, at least 60, at least 61, at least 62, at least 63, at least 64, at least 65, at least 66, at least 67, or at least 68, amino acids in the sequence of SEQ ID NO: 3 or any of SEQ ID NO: 4-23 are substituted an amino acid having evolutionarily neutral relatedness.
In another embodiment, the PBRT variants or PBRC variants described herein can also comprise a non-natural amino acid. As used herein, a non-natural amino acid can be, but is not limited to, an amino acid comprising a moiety where a chemical moiety is attached, such as an aldehyde- or keto-derivatized amino acid, or a non-natural amino acid that includes a chemical moiety. A non-natural amino acid can also be an amino acid comprising a moiety where a saccharide moiety can be attached, or an amino acid that includes a saccharide moiety. Examples of non-classical amino acids suitable for use with the methods and compositions described herein include, but are not limited to, D-isomers of the common amino acids, 2,4-diaminobutyric acid, alpha-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, gamma-Abu, epsilon-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosine, citrulline, homocitrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, beta-alanine, fluoro-amino acids, designer amino acids such as beta-methyl amino acids, C alpha-methyl amino acids, N alpha-methyl amino acids, and amino acid analogs in general.
The PBRT variants or PBRC variants described herein can also comprise one or more amino acid analog substitutions, e.g., unnatural amino acids such as alpha alpha-disubstituted amino acids, N-alkyl amino acids, lactic acid, and the like. These analogs include phosphoserine, phosphothreonine, phosphotyrosine, hydroxyproline, gamma-carboxyglutamate; hippuric acid, octahydroindole-2-carboxylic acid, statine, 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid, penicillamine, ornithine, citruline, .alpha.-methyl-alanine, para-benzoyl-phenylalanine, phenylglycine, propargylglycine, sarcosine, .epsilon.-N,N,N-trimethyllysine, .epsilon.-N-acetyllysine, N-acetylserine, N-formylmethionine, 3-methylhistidine, 5-hydroxylysine, .omega.-N-methylarginine, and other similar amino acids and imino acids and tert-butylglycine. The ability of PBRTs or PBRCs comprising an analog substitutions to bind to Ca2+, undergo reversible precipitation in the presence of Ca2+, or induce reversible precipitation of a purification moiety linked to the PBRT or PBRC using methods known to those skilled in the art.
The PBRT variants or PBRC variants described herein can further comprise polypeptide analogs, such as peptide mimetics (Fauchere J, Adv. Drug Res. 15:29 (1986); Veber D F and Freidinger R M, Trends Neurosci. 8:392-96 (1985); Evans B E et al., J. Med. Chem 30:1229-39 (1987)). Generally, peptidomimetics are structurally similar to a template polypeptide (i.e., a polypeptide that has a biological or pharmacological activity), such as the PBRTs or PBRCs described herein, but have one or more peptide linkages replaced by a linkage selected from the group consisting of: —CH.sub.2NH—, —CH.sub.2S—, —CH.sub.2-CH.sub.2-, —CH.dbd.CH-(cis and trans), —COCH.sub.2-, —CH(OH)CH.sub.2-, and —CH.sub.2SO—, by methods known in the art and further described in the following references: Spatola A F in “Chemistry and Biochemistry of Amino Acids, Peptides, and Proteins,” B. Weinstein, ed., Marcel Dekker, New York, p. 267 (1983); Spatola, A F, Vega Data (March 1983), Vol. 1, Issue 3, “Peptide Backbone Modifications” (general review); Morley J S, Trends Pharmcol. Sci. 1:463-68 (1980) (general review); Hudson D et al., Int. J. Pept. Prot. Res. 14:177-85 (1979) (—CH.sub.2NH—, CH.sub.2CH.sub.2-); Spatola A F et al., Life Sci. 38:1243-49 (1986) (—CH.sub.2-S); Hann M M, J. Chem. Soc. Perkin Trans. 1, 307-314 (1982) (—CH—CH—, cis and trans); Almquist R G et al., J. Med. Chem. 23:1392-98 (1980) (—COCH.sub.2-); Jennings-White C et al., Tetrahedron Lett. 23:2533-34 (1982) (—COCH.sub.2-); EP 0 045 665 (—CH(OH)CH.sub.2-); Holladay M W et al., Tetrahedron Lett., 24:4401-04 (1983) (—C(OH)CH.sub.2-); Hruby V J, Life Sci. 31:189-99 (1982) (—CH.sub.2-S—). One example of a non-peptide linkage is —CH.sub.2NH—.
Such polypeptide mimetics can have advantages over polypeptide embodiments, including, for example: more economical production, greater chemical stability, enhanced pharmacological properties (half-life, absorption, potency, efficacy, etc.), altered specificity (e.g., a broad-spectrum of biological activities), reduced antigenicity, and others. Labeling of peptidomimetics can involve covalent attachment of one or more labels, directly or through a spacer (e.g., an amide group), to non-interfering position(s) on the peptidomimetic that are predicted by quantitative structure-activity data and/or molecular modeling. Such non-interfering positions can be positions that do not from direct contacts with the macromolecules(s) to which the peptidomimetic binds to produce the therapeutic effect. Derivatization (e.g., labeling) of peptidomimetics can be done without substantially interfering with the desired biological or pharmacological activity of the peptidomimetic. The ability of any peptidomimetics to polypeptides can be assayed for the ability to bind 1,4-benzothiazepine or derivatives thereof using methods know to those skilled in the art.
Systematic substitution of one or more amino acids of the PBRTs or PBRCs described herein with a D-amino acid of the same type (e.g., D-lysine in place of L-lysine) can be used to generate additional PBRT and PBRT variants.
The following methods can be used in connection with the embodiments of the invention.

EXAMPLES

Example 1: Purification of PBRT or PBRC Linked Purification Moieties

17 tandem repeats of the amino acid sequence GGAGNDTLY (SEQ ID NO: 1) followed by a C-terminal “capping” sequence (the sequence is provided below) were fused to maltose binding protein. This construct was expressed in E. coli and the cells are lysed, creating a complex mixture of E. coli proteins and the Beta Roll tagged maltose binding protein. The mixture was exposed to 100 mM calcium chloride solution to form a precipitate form. The precipitate was pelleted and resuspended in calcium-free buffer. One precipitation cycle was sufficient to generate a relatively pure protein (FIG. 1). Multiple cycles can be used to achieve better purity.
The capping sequence used in this example is:

(SEQ ID NO: 3)

INAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQA

VDQAGIEKLVEAMAQYPD

Polypeptides comprising a 5 or 17 repeat C-capped precipitable beta-roll tags were expressed as MBP fusion proteins. 50 mM calcium was added to clarified cell lysates to induce precipitation of the polypeptides comprising a 5 or 17 repeat C-capped precipitable beta-roll tags. The precipitate was pelleted by centrifugation and the pellet was washed once and resuspended in buffer with 50 mM EGTA. The lysate, the supernatant after calcium addition, and the resuspended pellet were then run on an SDS-PAGE gel (FIG. 2). The results show that the methods described herein can be used to rapidly purify polypeptides comprising a 5 or 17 repeat C-capped precipitable beta-roll tags. Precipitation of purification moieties comprising a precipitable beta-roll tag can be confirmed by circular dichroism analysis (FIG. 3).
An intein domain can be coupled to the construct so that the cleavage reaction and subsequent second precipitation can be examined. Other proteins, in addition to maltose binding protein can be used with the purification protocols described herein.

Example 2: PBRT Sequence Heat Map

The heat map for the precipitable beta-roll tag sequences described herein was determined by using BLAST to find beta roll sequences similar to the metalloprotease of S. marcescens and then quantifying the frequency of amino acids at each of the nine positions after beta roll sequences were identified (FIG. 4). Certain positions in the precipitable beta-roll tag are not highly variable ( e.g. positions 1, 2, 4, 6, and 8), whereas other positions, exhibit moderate conservation. Positions 7, 9 are highly variable and can be substituted with any natural or non-natural amino acid.

Example 3: A Designed, Phase Changing PBRT-Based Peptide for Efficient Bioseparations

Non-chromatographic purification techniques are of interest since chromatography can be the most expensive step in protein purification (Przybycien et al., (2004). Alternative approaches can rely on targeted precipitation of the protein of interest. One approach is metal chelate affinity precipitation, where thermoresponsive copolymers can be used to specifically precipitate out poly-histidine tagged recombinant proteins (Balan et al., 2003; Kumar et al., 2003). Another purely protein-based approach is the use of thermoresponsive elastin-like peptides (ELPs) that consist of tandem repeats of the sequence VPGXG (SEQ ID NO: 1365) and precipitate with small temperature increases (McPherson et al., 1996; Meyer and Chilkoti. 1999). ELPs undergo an inverse phase transition and aggregation, which is thought to be driven by the exposure of hydrophobic patches in the peptides upon heating (Yamaoka et al., 2003). As part of a purification system, ELPs have been coupled to intein domains that have been genetically engineered into minimal self-cleaving units (Wood et al., 1999). When coupled, the ELP-intein system allows for a simple two-stage purification scheme. In the first step, precipitation of the ELP is triggered and the fusion protein is purified. Then, the intein is induced to cleave off the target protein and the ELP is again precipitated, leaving behind pure target protein in solution (Banki et al., 2005). While effective for many purification applications, the necessary heating of samples or the alternative use of high salt concentrations (Fong et al., 2009) can be problematic in many situations. Another protein-based non-chromatographic purification scheme developed by Ding et al. relies on calcium-dependent precipitation of an annexin B1 tag (Ding et al., 2007). As with ELPs, a self-cleaving intein is also incorporated in the fusion protein to remove the tag following purification.
The compositions and methods described herein relate to repeat scaffolds for protein engineering applications. Repeat scaffolds can have repetitive secondary structures (Courtemanche and Barrick 2008; Grove et al., 2008). Some repeat scaffolds can be engineered for biomolecular recognition, for example, the ankyrin repeats (Binz et al., 2004). In certain aspects, the compositions and methods described herein relate to consensus design to improve the engineerability of such scaffolds. When used in connection with the compositions and methods described herein, consensus design can be used to identify a core repeating peptide unit (Mosavi et al., 2004; Main et al., 2003; Parmeggiani et al., 2008; Binz et al., 2003).
Described herein is a synthetic PBRT peptide, based on the natural repeat-in-toxin (RTX) domain that undergoes calcium-responsive, reversible precipitation. In certain embodiments, when coupled to the maltose binding protein (MBP), the calcium-responsive tag described herein can be used to purify a fusion protein. In certain embodiments where the MBP is appended to green fluorescent protein (GFP), β-lactamase, or a thermostable alcohol dehydrogenase (AdhD), these constructs can also be purified by calcium-induced precipitation. In certain embodiments, protease cleavage of the precipitating tag enables the recovery of pure and active target protein by cycling precipitation before and after cleavage.
The methods and compositions described herein relate to novel stimulus-responsive repeat scaffolds for protein engineering based on the calcium-responsive repeat-in-toxin (RTX) domain. The RTX domain is found in proteins secreted through the bacterial type 1 secretion system (Holland et al., 2005). The domain consists of repeats of the consensus amino acid sequence GGXGXDXUX (SEQ ID NO: 1366), where X is variable and U is a hydrophobic amino acid. One RTX domain is the block V RTX domain from the adenylate cyclase toxin (CyaA) of B. pertussis. The domain is intrinsically disordered in the absence of calcium and forms a β roll structure (FIG. 13A) in the presence of calcium (Chenal et al., 2009). The block V RTX domain retains its reversible calcium-responsiveness even when expressed separately from the larger protein (Bauche et al., 2006; Blenner et al., 2010). Previous attempts have been made to use RTX domains in protein engineering, including incorporation into mesh networks, design of synthetic RTX peptides, and generation of hydrogel-forming RTX domains (Lilie et al., 2000; Ringler, P. and G. E. Schulz. 2003; Scotter et al., 2007; Dooley et al., 2012).
In certain aspects, the compositions and methods described herein relate to the design of consensus RTX domains. The frequency of amino acids at each position of the nine amino acid repeat unit from a set of RTX-containing proteins have examined and resulted in the identification of a consensus PBRT sequence GGAGNDTLY (SEQ ID NO: 1) (FIG. 13B). A library of consensus constructs consisting of 5, 9, 13, or 17 repeats of the PBRT consensus unit was created. Upon purification of a number of these constructs, many of them were observed to precipitate in the presence of calcium. Therefore, it was decided to explore the possibility of using these consensus precipitable β roll tags (PBRTs) as a tool for bioseparation.
Reported herein is the use of PBRTs to purify recombinant proteins. A maltose binding protein (MBP)-PBRT17 fusion was first purified as a proof of principle. This MBP-PBRT17 construct was fused to green fluorescent protein (GFP), which was used as a reporter during initial purification experiments. β-lactamase and a thermostable alcohol dehydrogenase (AdhD) were also fused to demonstrate the feasibility of purifying enzymatic proteins. In certain embodiments, a specific protease site was engineered downstream of the tag to show that target proteins can be fully purified by protease cleavage while retaining their activity.
Oligonucleotides suitable for used in connection with the methods and compositions described herein are in Table 1.

TABLE 1

Oligonucleotides

Name	Sequence

cons_beta_1	5′_ggcggtgcgggcaacgataccctgtatggtggcgccgggaatgacacattatacggaggtgctgg
	caatgatacgctgtatggcggagcaggtaacgac_3′ (SEQ ID NO. 1345)

cons_beta_2	5′_attcccagcaccgccataaagggtatcgttgcctgcccccccatacagcgtgtcgttaccggcgccc
	ccatacaaagtgtcgttacctgctccgc_3′ (SEQ ID NO. 1346)

cons_beta_3	5′_ggcggtgctgggaatgacacactgtacggcggggcgggtaacgataccctctatggtggtgctgg
	caatgatacactgtat_3′ (SEQ ID NO. 1367)

cons1_AvaI_F	5′_attaaaaactcggggatgatgatgatgacaagggcggtgcggg_3′ (SEQ ID NO. 1347)

cons9_BseRI	5′_tttttaataagcttgaggagtattattaatacagtgtatcattgccagcac_3′ (SEQ ID NO.
HindIII_R	1348)

cons5_BseRI	5′_tttttaataagcttgaggagtattattaatacagcgtgtcgttaccg_3′ (SEQ ID NO. 1349)
HindIII_R

cons1_BtsCI_F
	5′_attaaaaaggatgatggcggtgcggg_3′ (SEQ ID NO. 1350)

cons4_BseRI_	5′_tttttaataagcttgaggagtattattaatacaaagtgtcgttacctgctc_3′ (SEQ ID NO.
HindIII_R	1351)

cons8_BseRI_	5′_tttttaataagcttgaggagtattattaatagagggtatcgttacccgc_3′ (SEQ ID NO.
HindIII_R	1352)

GFP_BseRI_F	5′_aatatatagaggagataataatatatgagtaaaggagaagaacttttcactggagt_3′ (SEQ ID
	NO. 1353)

GFP_HindIII_	5′_tattataaagcttttatttgtatagttcatccatgccatgtgtaat_3′ (SEQ ID NO. 1354)
R

blac_BseRI_F
	5′_aatatatagaggagataataatatatgagtattcaacatttccgtgtcgc_3′ (SEQ ID NO.
	1355)

blac_HindIII_R	5′_tattattaagcttttattaccaatgcttaatcagtgaggcacc_3′ (SEQ ID NO. 1356)

AdhD_BserI_F	5′_aaagaggaggatcatgaatatggcaaaaagggtaaatgcattcaacgacc_3′ (SEQ ID
	NO. 1357)

AdhD_HindIII_	5′_agtgccaagatttattacacacacctccttgccatctctctatcctc_3′ (SEQ ID NO. 1358)
R

blac_entero_
	5′_aaagaggaggatcatgaatgatgatgatgacaagatgagtattcaacatttccgtgtcgcccttattc_
BseRI_F	3′ (SEQ ID NO. 1359)

AdhD_entero_	5′_aaagaggaggatcatgaatgatgatgatgacaagatggcaaaaagggtaaatgcattcaacgacc
BseRI	F_3′ (SEQ ID NO. 1360)

entero_KOI_F	5′_cctcggggatgatggtgacaagggcggtgc_3′ (SEQ ID NO. 1361)

entero_KOI_R	5′_gcaccgccatgtcaccatcatccccgagg_3′ (SEQ ID NO. 1362)

entero_KOII_F	5′_ggggatgatggtgagcagggcggtgcgggc_3′ (SEQ ID NO. 1363)

entero_KOII_R	5′_gcccgcaccgccctgctcaccatcatcccc_3′ (SEQ ID NO. 1364)

Sequences are provided for all oligonucleotides used for cloning experiments.

Four differently sized MBP-PBRT fusions were prepared consisting of 5, 9, 13, or 17 repeats of the consensus PBRT sequence (named PBRTS, PBRT9, PBRT13, and PBRT17). In order to generate the DNA fragment for PBRT9, three oligonucleotides were synthesized: cons_β_1, cons_β_2, and cons_β_3. One ng each of these oligonucleotides was mixed along with the primers cons1_AvaI_F and cons9_BseRI_HindIII_R. PCR was performed and a clean product was obtained and gel extracted. This fragment was digested with AvaI and HindIII and cloned into the similarly digested pMAL_c4E vector to generate pMAL_BRT9.
To generate the PBRTS construct, pMAL_BRT9 was used as a template for PCR with the primers cons 1_AvaI_F and cons5_BseRI_HindIII_R. This product was digested with AvaI and HindIII and cloned into the pMAL_c4E vector producing pMAL_BRT5.
BRT13 was produced by concatenation of four additional repeats to PBRT9. Concatenations were achieved using a recursive ligation technique similar to those previously described (Meyer et al., 2002; McDaniel et al., 2010). This four repeat insert was amplified using primers cons1_BtsCI_F and cons4_BseRI_HindIII_R. The product was digested with BtsCI and HindIII and then cloned into pMAL_BRT9 cut with BseRI and HindIII to yield pMAL_BRT13. PBRT17 was produced analogously to PBRT13, except that the reverse primer cons8_BseRI_HindIII_R was used instead of cons4_BseRI_HindIII_R.
The emGFP gene was amplified from the Invitrogen pRSET/emGFP vector using primers GFP_BseRI_F and GFP_HindIII_R. The β-lactamase gene was amplified from the pMAL_c4E vector using primers βlac_BseRI_F and βlac_HindIII_R. The AdhD gene was amplified out of pWUR85 using primers AdhD_BserI_F and AdhD_HindIII_R (Campbell et al., 2010). All three of these inserts were digested with BseRI and HindIII and cloned into similarly digested pMAL_BRT17 to yield pMAL_BRT17_GFP, pMAL_BRT17_βlac and pMAL_PBRT17_AdhD.
The native enterokinase site in the pMAL_c4E vector, which sits between MBP and PBRT17, was knocked out in the pMAL_BRT17_βlac and pMAL_BRT17AdhD plasmids. Two rounds of site-directed mutagenesis were required to change the native recognition site, DDDDK (SEQ ID NO: 1368), to DDGEQ (SEQ ID NO: 1369), which was shown to be resistant to cleavage. A novel enterokinase recognition site was also engineered downstream of PBRT17 in these constructs to allow for purification of the untagged protein of interest. Full plasmid maps of all cloned constructs are available in FIG. 12.
E. coli cells were used for expression and cloning. One liter cultures of TB supplemented with 100 μg/mL ampicillin and 0.2% glucose were inoculated with 10 mL of overnight culture. Cultures were grown at 37° C. with shaking at 225 RPM to an approximate OD600 of 0.5 and induced with 0.3 mM IPTG. Cells harboring pMAL_BRT17 and pMAL_BRT17_βlac were allowed to express for an additional two hours and then harvested. Cultures transformed with pMAL_BRT17_GFP were transferred to a shaker at 25° C. and allowed to express for an additional 16 h and then harvested as no fluorescence was observed when expressed at 37° C. Cultures transformed with pMAL_BRT17_AdhD were allowed to express at 37° C. for an additional 16 h as previously reported (Campbell et al., 2010). Cells were harvested after expression and resuspended in 1/20 culture volume of 50 mM tris-HCl, pH 7.4 for precipitation purification. For amylose resin purification, cells were resuspended in 1/20 culture volume of MBP column buffer (20 mM tris-HCl, 200 mM NaCl, 1 mM EDTA, pH 7.4). In both cases, cells were subsequently lysed via 150 s. Lysate was then clarified by centrifugation at 15,000 g for 30 min at 4° C. For amylose resin purification, clarified lysate was diluted with five volumes of column buffer and purified as previously described (Blenner et al., 2010). All subsequent steps were performed at room temperature.
For precipitation purification, clarified lysate was added to a concentrated calcium stock according to the data presented in FIG. 14. For example, for precipitation of MBP-PBRT17 lysate in 100 mM CaCl2, 950 μL, of clarified lysate was added to 50 μL, of 2 M CaCl2 solution. The sample was promptly mixed by gentle pipetting, allowed to sit at room temperature for 2 min and then centrifuged at 16,000 g in a microcentrifuge for 2 min. The supernatant was carefully removed and the pellet was resuspended in the same tris buffer by gentle pipetting. The turbid solution was centrifuged and washed for four additional cycles. For the final step, the pellet was resuspended in tris buffer with a concentration of EGTA equivalent to the original calcium concentration. Gentle pipetting was sufficient to cause the sample to redissolve as confirmed by observation and the lack of a precipitate upon subsequent centrifugation.
Concentrations of all purified proteins were determined by 280 nm absorbance using extinction coefficients predicted by ExPASy (www expasy.org). All extinction coefficients are provided in Supplementary Table 3. Recovery of MBP-PBRT17 by either amylose resin purification or precipitation was determined solely using this method.

TABLE 2

Calculated Extinction Coefficients

	Construct	ε, M−1 cm−1

	MBP-PBRT17	91680
	MBP-PBRT17-GFP	113695
	MBP-PBRT17-βlac	119765
	MBP-PBRT17-AdhD	144175
	AdhD	52370

Calculated molar extinction coefficients are given for all protein constructs. The ExPASy ProtParam tool was used for calculation.
MBP-PBRT17-GFP recoveries were estimated by comparing fluorescence emission intensity at 509 nm with excitation at 487 nm. 100-fold dilutions of both clarified lysate and purified protein were made for fluorescence measurements. Purified proteins were resuspended in the same volume as the lysate from which they were extracted, so signals were compared directly.
For estimation of MBP-PBRT17-βlac recovery, protein was added to a nitrocefin solution and the absorbance at 486 nm was tracked corresponding to the hydrolysis of nitrocefin. 500 μL of nitrocefin solution was prepared by placing three nitrocefin disks in 450 μL 50 mM tris-HCl, pH 7.4 and 50 μL DMSO. In each sample well, 50 μL of this solution was mixed with 90 μL of the same tris buffer and 10 μL of protein sample. For each sample tested, serial dilutions from 1× to 1000× were prepared from lysate and purified protein. Initial rates were determined by measuring the change in absorbance at 486 nm over the first 20% of the change in signal between the starting absorbance and the end absorbance. The same nitrocefin stock solution was used for all samples to account for variations in concentration.
MBP-PBRT17-AdhD recovery was also evaluated by enzymatic activity using a protocol previously described (Campbell et al., 2010). Since this AdhD was isolated from the hyperthermofile Pyrococcus furiosus, all samples were heat treated at 80° C. for 1 h prior to evaluating activity. All assays were performed at saturated conditions of both cofactor and substrate, 0.5 mM NAD+ and 100 mM 2,3-butanediol, respectively. Reaction mixtures containing 2,3-butanediol and protein sample in 50 mM glycine pH 8.8 were incubated at 45° C. in a 96 well UV microplate in a spectrophotometer. Reactions were initiated by the addition of NAD+. Initial rates were calculated by following the production of NADH at 340 nm. Specific activity of cleaved AdhD was calculated using an NADH extinction coefficient (ε=6.22 mM-1 cm-1).
In order to identify the consensus RTX sequence, a database of RTX containing proteins was constructed by searching the UniProt (www uniprot.org) database for hemolysin-type calcium binding domains. Individual repeats were identified and the frequency of amino acids at each of the nine repeat positions was determined (FIG. 13B). From this result, the repeat sequence GGAGNDTLY (SEQ ID NO: 1) was identified as the consensus sequence. For a few of these positions, other amino acids were found with nearly equal frequency. However, as this sequence was found to be effective for purification, further investigation on sequence variation was not performed. A variety of synthetic RTX domains of different lengths (PBRT5, PBRT9, PBRT13, PBRT17) were prepared as fusions to the C terminus of MBP, with subscripts denoting the number of repeats. These lengths were chosen as they reflect the variability of naturally occurring RTX domains. Upon the addition of calcium to the purified PBRT17 construct, there was significant precipitation out of solution, which was reversed upon the addition of the chelating agent EGTA.
In order to more thoroughly characterize the observed precipitation behavior, cells were induced to express the four MBP-PBRT constructs. Clarified cell lysates were titrated with calcium to assess precipitation behavior by mixing with CaCl2 solution at the indicated concentrations, followed by centrifugation, and measurement of the mass of the pellet (FIG. 14). Due to possible variations in cell growth rates and densities, all cultures were started from saturated overnight cultures and induced simultaneously. Both PBRT13 and PBRT17 precipitated when calcium concentrations exceeded 25 mM. Some precipitation was observed from PBRT5 and PBRT9 lysate, similar to what was observed with control cell lysate. Addition of an equivalent concentration of EGTA allowed the pellets to quickly dissolve again upon gentle pipetting.
While both PBRT13 and PBRT17 precipitated upon calcium addition, PBRT17 formed a pellet that was easier to clarify and was therefore selected for further examination. Three additional constructs were prepared by fusing MBP-PBRT17 to the N terminus of GFP, β-lactamase, and AdhD (named MBP-PBRT17-GFP and MBP-PBRT17-βlac, MBP-PBRT17-AdhD respectively). These three proteins were fused to MBP to allow for amylose resin chromatography purification as a comparison technique. GFP was chosen as a reporter protein for initial purification experiments to track the location of the PBRT. β-lactamase and AdhD were chosen as they are well characterized enzymes whose activity can be measured with straightforward assays.
The folding of RTX domains into β rolls is highly calcium specific. Therefore, investigation was performed to determine whether the precipitation behavior observed was also calcium-specific. To test this, MBP-PBRT17-GFP was purified on an amylose resin and diafiltered into salt-free tris buffer. Diafiltration was used as proteins are purified in high salt buffer for the amylose resin step and it was observed that PBRT precipitation was significantly in high salt. This is consistent with previous observations that RTX calcium affinity is reduced with increasing salt concentration (Szilvay et al., 2009). Solutions of various salts were added to final concentrations of 100 mM. The samples were then gently mixed by pipetting, allowed to sit for 2 min, and centrifuged at 16,000 g in a microcentrifuge for 2 min. Tubes were then inverted and the presence of a pellet at the top was indicative of precipitation (FIG. 15). PBRT precipitation was observed to be calcium-specific, with near complete precipitation of MBP-PBRT17-GFP (as indicated by the remaining color in solution) in the presence of calcium and no precipitation with other salts.
For all 4 constructs tested, calcium concentrations greater than 25 mM were found to cause precipitation of the fusion protein. To assess the ideal calcium concentration, all 4 constructs were precipitated from 1 mL of clarified cell lysate in 25, 50, 75, and 100 mM CaCl2. Pellets were washed in salt-free tris buffer five times. Pellets were broken up upon washing, but did not redissolve until exposed to an equivalent concentration of EGTA after the final wash. The 100 mM CaCl2 samples were found to not fully redissolve, so only lower CaCl2 concentrations were tested further. A slight increase in recovery was observed at 75 mM CaCl2 (as compared with lower CaCl2 concentrations) as confirmed by SDS-PAGE. All 4 constructs were subsequently purified by precipitation with 75 mM CaCl2 and SDS-PAGE gels were run after 5 washes (FIG. 16). No significant difference was found with increasing number of washes, so further quantification and recovery measurements were performed on samples washed five times. To confirm scalability, the analogous protocol was also performed on 50 mL lysate, and comparable results were obtained. Additionally, the reversibility of the precipitation process was tested. It was found that addition of calcium to the redissolved pellet in EGTA solution did yield a pellet once again. Full pellet size was only recovered after dialysis into EGTA-free buffer.
The recovery and functionality of the purified proteins after precipitation was then quantified. To assess recovery of MBP-PBRT17, the theoretically determined extinction coefficient was used to estimate concentration by absorbance at 280 nm (Gill and Vonhippel, 1989). Results from purifying the construct on an amylose resin were compared with PBRT precipitation. For MBP-PBRT17-GFP, recoveries were calculated as the percentage of fluorescence signal of purified sample compared with lysate (this was normalized against control lysate). Along with total protein recoveries estimated by UV absorbance, recoveries of both MBP-PBRT17-βlac and MBP-PBRT17-AdhD were estimated by comparing lysate activity to the activity of these constructs after purification. MBP-PBRT17-βlac recoveries were calculated using activity measured by tracking the absorbance at 486 nm for the hydrolysis of nitrocefin. MBP-PBRT17-AdhD recoveries were calculated by tracking NADH formation at 340 nm in saturating conditions of both substrate and cofactor. Results of these trials are shown in Table 3.

TABLE 3

Recovery Data for three constructs tested.

MBP-

MBP-PBRT17-GFP

MBP-PBRT17-βlac

PBRT17

Fold

MBP-PBRT17-AdhD

Calcium,	Fold versus	versus		versus	Activity	Fold versus	Activity
mM	Resin	Resin	Fluorescence	Resin	Recovered	Resin	Recovered

25	2.0 ± 0.1	2.8 ± 0.1	61 ± 3%	4.1 ± 0.1	1.6 ± 0.1%	1.6 ± 0.1	3.8 ± 0.5%
50	2.3 ± 0.1	3.7 ± 0.1	86 ± 6%	5.3 ± 0.2	4.0 ± 0.1%	1.7 ± 0.1	4.7 ± 0.7%
75	2.2 ± 0.2	2.8 ± 0.3	78 ± 8%	5.1 ± 0.2	3.4 ± 0.1%	2.2 ± 0.1	8.3 ± 1.4%

“Fold versus Resin” denotes protein quantity recovered relative to amylose resin for equivalent loading amount. For MBP-PBRT17-GFP, MBP-PBRT17-βlac, and MBP-PBRT17-AdhD fluorescence and activity are the respective properties relative to clarified lysate. Errors represent standard deviations. All data were collected in triplicate.
For MBP-PBRT17, calcium precipitation recovers about double the amount of protein as compared with amylose resin purification. For MBP-PBRT17-GFP, up to 86% recovery of fluorescence was observed. MBP-PBRT17-βlac recovery from the lysate was not as high, but was still 5-fold better than the amylose resin, yielding a significant quantity of protein. Similar results were also observed for MBP-PBRT17-AdhD, although the yields were not quite as high compared with the resin (2-fold improvement). The overall values of the activities recovered in Table 4 were all larger than the values obtained using the amylose resin purification. It is also possible that measuring activity in crude extracts may introduce error beyond what was accounted for in the measurement of endogenous hydrolysis (β-lactamase) and reduction (AdhD). Table 4 lists the absolute yield of each fusion protein based on UV absorption at 280 nm. All fusion proteins were shown to be purified in high yields.

TABLE 4

Absolute Protein Yields
Absolute Yield (mg/L)

				MBP-
	MBP-	MBP-	MBP-	PBRT17-
Calcium, mM	PBRT17	PBRT17-GFP	PBRT17-βlac	AdhD

25	268 ± 11	333 ± 12	124 ± 3	198 ± 3
50	305 ± 14	434 ± 17	160 ± 7	273 ± 9
75	295 ± 26	336 ± 40	176 ± 5	214 ± 6

Amount of protein recovered for each fusion construct after precipitation and washing. Values were determined using UV absorbance at 280 nm and calculated extinction coefficients available in the Table 2. All data were collected in triplicate and errors represent standard deviations.
In certain embodiments, the PBRTs described herein can be coupled with a cleavage tag to separate the protein of interest from the PBRT. The pMAL_c4E vector used for these assays contains a cleavable enterokinase site between the MBP and PBRT. This recognition sequence was removed via site-directed mutagenesis. A new enterokinase site was engineered between the PBRT and the protein of interest for MBP-PBRT17-βlac and MBP-PBRT17-AdhD. Therefore, as a proof of principle, precipitation purified MBP-PBRT17-βlac and MBP-PBRT17-AdhD was subjected to overnight cleavage by enterokinase digestion. Calcium was then added directly to the cleavage reaction to precipitate MBP-PBRT17, thereby separating the tag from the protein of interest following centrifugation. This is shown in FIG. 17 for MBP-PBRT17-AdhD, showing pure, soluble protein by SDS-PAGE. Recoveries of 93±7% were obtained by tracking UV absorbance at 280 nm, meaning 93% of the AdhD in the precipitation purified sample was recovered after cleavage and reprecipitation of the tag. Specific activity of the purified enzyme was also calculated to be 20.2±1.3 min-1, which is similar to what has been previously reported, indicating this system has little to no effect on the activities of purified proteins (Campbell et al., 2010). However, in the case of MBP-PBRT17-βlac, the cleaved β-lactamase remained in the insoluble fraction following enterokinase cleavage and calcium precipitation. Upon further investigation it was found that β-lactamase will precipitate in high calcium concentrations. As a control experiment, similar behavior was observed in recombinant β-lactamase. In 75 mM CaCl2, an insoluble pellet was formed upon centrifugation. Activity assays confirmed a significant amount of active protein in the insoluble fraction. In certain embodiments, the protease used could be fused to the precipitating PBRT or a self-cleaving intein could be incorporated. Fusing the protease to the PBRT can be used for its removal from the target protein in the final precipitation. A self-cleaving intein can also be used to fulfill a similar function. PBRT can also precipitate without being fused to the MBP, indicating that the MBP is not essential for this system. In certain embodiments, the MBP may be useful for improving protein expression levels.
The results described herein show a correlation between length and precipitation (FIG. 14). However, there has not been extensive work in studying the role of the number of repeats on RTX behavior. The impact of altering the number of native RTX repeats in the block V CyaA RTX domain of B. pertussis was previously examined without significant size effect and C-terminal capping was required for calcium-responsiveness (Shur and Banta, 2012). As for past efforts to design synthetic RTX domains, the synthetic domains created by Scotter et al. consisted of 4 RTX repeats and those prepared by Lilie et al. consisted of 8 repeats (Lilie et al., 2000; Scotter et al., 2007). The peptides create by Lilie et al. were weakly calcium-responsive, while those of Scotter et al. were only lanthanum-responsive and formed partially insoluble filaments in the presence of lanthanum. In general, 13 sheets are prone to aggregation and nature uses various strategies to ensure solubility of proteins containing these motifs (Richardson and Richardson, 2002). PBRTs may be a balance between this tendency and the calcium-responsiveness of the β roll.
The technique described herein provides a new stimulus-responsive phase-changing peptide useful in a range of applications similar to those for which ELPs have been used, such as recombinant protein purification or the creation of “smart” biomaterials. The PBRTs described herein possesses certain advantages over ELPs and annexin B1 since precipitation is simpler to achieve and the PBRT peptide is significantly smaller. Additionally, PBRT17 precipitates in as little as 25 mM CaCl2 at room temperature, compared to the larger ionic strength and higher temperature increases required for ELP precipitation. Precipitation also occurs instantaneously, whereas annexin B1-based systems require a 2 h incubation period at 4° C. Overall, PBRTs offer a new tool for rapid purification of recombinant proteins. The protocol described here can be performed to obtain purified fusion protein from lysate in only a few minutes. Further optimization of the PBRT system should enable the use of specific proteases to purify target proteins and further improve the precipitation and resolubilization process, greatly enhancing the ability to rapidly purify recombinant proteins.
Although the invention has been described and illustrated with respect to exemplary embodiments thereof, it should be understood by those skilled in the art that the foregoing and various other changes, omissions and additions may be made therein and thereto, without parting from the spirit and scope of the present invention.

Claims

What is claimed is:

1. A method for purifying a precipitable beta roll cassette (PBRC) linked purification moiety, the method comprising:

(a) expressing the PBRC linked purification moiety in an expression system,

(b) collecting the PBRC linked purification moiety in a first medium,

(c) adding Ca2+ to the first medium so as to induce precipitation of PBRC linked purification moiety, and

(d) removing unprecipitated material from the medium from the precipitated PBRC linked purification moiety.

2. The method for purifying a PBRC linked purification moiety according to claim 1, the method further comprising:

(e) resuspending the PBRC linked purification moiety in a second medium having a lower than the free Ca2+ concentration than the free Ca2+ concentration obtained after step (c).

3. The method of claim 2 wherein a calcium chelator is added to the second medium of step (e).

4. The method of claim 2, wherein steps (c) to (e) are repeated one or more times.

5. The method of claim 1, further comprising a step of removing precipitated material between step (b) and step (c).

6. The method of claim 1, wherein the PBRC comprises a cleavage site between the PBRC and the purification moiety.

7. The method of claim 1, further comprising steps of:

(i) cleaving the PBRC linked purification moiety so as to separate the purification moiety from the PBRC,

(ii) adding Ca2+ to the medium so as to induce precipitation of the PBRC, and

(iii) isolating the unprecipitated purification moiety.

8. The method of claim 6, wherein the cleavage site is selected from the group consisting of an intein cleavage site, a Factor Xa cleavage site, a thrombin cleavage site, an enterokinase cleavage site, or a signal peptidase cleavage site.

9. The method of claim 1, wherein the PBRC comprises at least two beta roll tags (PBRTs).

10. The method of claim 9, wherein the at least two PBRTs each comprise the amino acid sequence of SEQ ID NO: 1.

11. The method of claim 9, wherein the at least two PBRTs are independently any of:

(a) a polypeptide having the amino acid sequence of SEQ ID NO: 1, or

(b) a polypeptide having the amino acid sequence of any of SEQ ID NOs 25-1337.

12. The method of claim 9, wherein the at least two PBRTs are independently any of:

(a) a polypeptide having the amino acid sequence of SEQ ID NO: 1, or

(b) a polypeptide having the amino acid sequence of any of SEQ ID NOs 25-1337; or

(c) a polypeptide comprising the amino acid sequence GXXXXXXXX, wherein,

i. the X at position 2 is an amino acid selected from the group consisting of glycine, asparagine or aspartic acid, and

ii. the X at position 3 is an amino acid selected from the group consisting of alanine, glycine, aspartic acid, glutamic acid, leucine or asparagine,

and

iii. the X at position 4 is an amino acid selected from the group consisting of glycine or alanine, and

iv. the X at position 5 is an amino acid selected from the group consisting of asparagine, aspartic acid, alanine, or serine, and

v. the X at position 6 is an amino acid selected from the group consisting of aspartic acid or asparagine,

vi. the X at position 7 is an amino acid selected from the group consisting of threonine, isoleucine, valine, or leucine, and

vii. the X at position 8 is an amino acid selected from the group consisting of leucine, isoleucine, or phenylalanine, and

viii. the X at position 9 is an amino acid selected from the group consisting of tyrosine, isoleucine, valine, phenylalanine, threonine, asparagine, aspartic acid, lysine or serine.

13. The method of claim 1, wherein the PBRC comprises a capping sequence.

14. The method of claim 1, wherein the PBRC comprises a stabilizing peptide.

15. The method of claim 6, wherein the cleavage site is located N-terminally or C-terminally to the PBRC.

16. An expression vector comprising, as arranged from 5′ to 3′, a promoter, a nucleic acid sequence encoding a precipitable beta roll cassette (PBRC) comprising at least two beta roll tags (PBRTs), wherein the PBRC precipitates in response to binding of calcium by the at least two PBRTs, and at least one cloning site.

17. An expression vector comprising, as arranged from 5′ to 3′, a promoter, at least one cloning site, and a nucleic acid sequence encoding a precipitable beta roll cassette (PBRC) comprising at least two beta roll tags (PBRTs), wherein the nucleic acid sequence encoding the at least two PBRTs encodes at least the amino acid sequence of SEQ ID NO: 1.

18. The expression vector according to claim 17, further comprising at least a second cloning site.

19. The expression vector according to claim 16, wherein the nucleic acid sequence encoding the at least two PBRTs encodes at least the amino acid sequence of SEQ ID NO: 1.